diff --git a/screen2.0/.eslintrc.json b/screen2.0/.eslintrc.json deleted file mode 100644 index bffb357a..00000000 --- a/screen2.0/.eslintrc.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "extends": "next/core-web-vitals" -} diff --git a/screen2.0/eslint.config.js b/screen2.0/eslint.config.js new file mode 100644 index 00000000..f51117a1 --- /dev/null +++ b/screen2.0/eslint.config.js @@ -0,0 +1,23 @@ +import js from '@eslint/js' +import reactHooks from 'eslint-plugin-react-hooks' +import reactRefresh from 'eslint-plugin-react-refresh' +import tseslint from 'typescript-eslint' + +export default tseslint.config( + { ignores: ['dist'] }, + { + extends: [js.configs.recommended, ...tseslint.configs.recommended], + files: ['**/*.{ts,tsx}'], + plugins: { + 'react-hooks': reactHooks, + 'react-refresh': reactRefresh, + }, + rules: { + ...reactHooks.configs.recommended.rules, + 'react-refresh/only-export-components': [ + 'warn', + { allowConstantExport: true }, + ], + }, + }, +) diff --git a/screen2.0/next.config.js b/screen2.0/next.config.mjs similarity index 78% rename from screen2.0/next.config.js rename to screen2.0/next.config.mjs index 5df35da0..0db5200d 100644 --- a/screen2.0/next.config.js +++ b/screen2.0/next.config.mjs @@ -1,7 +1,8 @@ -/** @type {import('next').NextConfig} */ - -let assetPrefix = '' -let basePath = '' +// @ts-check + +/** + * @type {import('next').NextConfig} + */ const nextConfig = { // output: "export", @@ -12,8 +13,8 @@ const nextConfig = { }, generateEtags: false, trailingSlash: false, - assetPrefix: assetPrefix, - basePath: basePath, + assetPrefix: '', + basePath: '', logging: { fetches: { fullUrl: true, @@ -32,4 +33,4 @@ const nextConfig = { } } -module.exports = nextConfig +export default nextConfig diff --git a/screen2.0/package.json b/screen2.0/package.json index 699dfbd1..937c8d7d 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -2,6 +2,7 @@ "name": "screen2.0", "version": "0.0.5", "private": true, + "type": "module", "scripts": { "dev": "next dev", "build": "next build", @@ -43,10 +44,10 @@ "@emotion/cache": "^11.13.1", "@emotion/react": "^11.13.3", "@emotion/styled": "^11.13.0", - "@mui/icons-material": "^6.1.1", - "@mui/lab": "^6.0.0-beta.10", - "@mui/material": "^6.1.1", - "@mui/material-nextjs": "^6.1.1", + "@mui/icons-material": "^6.1.5", + "@mui/lab": "6.0.0-beta.13", + "@mui/material": "^6.1.5", + "@mui/material-nextjs": "^6.1.5", "@parcel/watcher": "^2.4.1", "@types/node": "^22.6.1", "@types/react": "^18.3.8", @@ -58,8 +59,6 @@ "@weng-lab/ts-ztable": "^4.0.1", "autoprefixer": "10.4.20", "bpnet-ui": "^0.3.8", - "eslint": "9.11.1", - "eslint-config-next": "14.2.13", "graphql": "^16.9.0", "jubilant-carnival": "^0.6.0", "logots-react": "^0.2.0", @@ -79,13 +78,20 @@ "uuid": "^10.0.0" }, "devDependencies": { + "@eslint/js": "^9.13.0", "@graphql-codegen/cli": "^5.0.2", "@graphql-codegen/client-preset": "^4.3.3", "@graphql-typed-document-node/core": "^3.2.0", + "eslint": "9.13.0", + "eslint-config-next": "15.0.1", + "eslint-plugin-react": "^7.37.2", + "eslint-plugin-react-hooks": "^5.0.0", + "eslint-plugin-react-refresh": "^0.4.14", "file-loader": "^6.2.0", "lint-staged": "^15.2.10", "prettier": "^3.3.3", "typescript": "5.6.2", + "typescript-eslint": "^8.11.0", "webpack": "^5.94.0", "webpack-cli": "^5.1.4" }, @@ -104,5 +110,5 @@ "not ie <= 11", "not op_mini all" ], - "packageManager": "yarn@3.5.0+sha512.2dc70be5fce9f66756d25b00a888f3ca66f86b502b76750e72ba54cec89da767b938c54124595e26f868825688e0fe3552c26c76a330673343057acadd5cfcf2" + "packageManager": "yarn@4.5.1" } diff --git a/screen2.0/postcss.config.js b/screen2.0/postcss.config.cjs similarity index 100% rename from screen2.0/postcss.config.js rename to screen2.0/postcss.config.cjs diff --git a/screen2.0/src/app/applets/gene-expression/BarPlot.tsx b/screen2.0/src/app/applets/gene-expression/BarPlot.tsx new file mode 100644 index 00000000..49f5db1a --- /dev/null +++ b/screen2.0/src/app/applets/gene-expression/BarPlot.tsx @@ -0,0 +1,165 @@ +import React, { useCallback, useMemo, useRef } from 'react'; +import { Bar } from '@visx/shape'; +import { scaleBand, scaleLinear } from '@visx/scale'; +import { AxisTop } from '@visx/axis'; +import { Group } from '@visx/group'; +import { Text } from '@visx/text'; +import { useParentSize } from '@visx/responsive'; +import { defaultStyles as defaultTooltipStyles, useTooltip, TooltipWithBounds, Portal } from '@visx/tooltip'; + +export interface BarData { + category: string; + label: string; + value: number; + color?: string; + metadata?: T; +} + +export interface BarPlotProps { + data: BarData[]; + SVGref?: React.MutableRefObject + topAxisLabel?: string; + onBarClicked?: (bar: BarData) => void; + TooltipContents?: (bar: BarData) => React.ReactNode +} + +const VerticalBarPlot = ({ + data = [], + SVGref, + topAxisLabel, + onBarClicked, + TooltipContents +}: BarPlotProps) => { + const { parentRef, width: ParentWidth } = useParentSize({ debounceTime: 150 }); + const { tooltipOpen, tooltipLeft, tooltipTop, tooltipData, hideTooltip, showTooltip } = useTooltip>({}); + const requestRef = useRef(null); + const tooltipDataRef = useRef<{ top: number; left: number; data: BarData } | null>(null); + + const handleMouseMove = useCallback((event: React.MouseEvent, barData: BarData) => { + tooltipDataRef.current = { + top: event.pageY, + left: event.pageX, + data: barData, + }; + if (!requestRef.current) { + requestRef.current = requestAnimationFrame(() => { + if (tooltipDataRef.current) { + showTooltip({ + tooltipTop: tooltipDataRef.current.top, + tooltipLeft: tooltipDataRef.current.left, + tooltipData: tooltipDataRef.current.data, + }); + } + requestRef.current = null; + }); + } + }, [showTooltip]); + + const width = useMemo(() => Math.max(500, ParentWidth), [ParentWidth]) + + /** + * @todo it'd be nice to somehow extract these from what is passed to the component. This is hardcoded to fit the gene expression data + */ + const spaceForTopAxis = 50 + const spaceOnBottom = 20 + const spaceForCategory = 120 + const spaceForLabel = 280 + + const height = data.length * 20 + spaceForTopAxis + spaceOnBottom + + // Dimensions + const xMax = width - spaceForCategory - spaceForLabel; + const yMax = height - spaceForTopAxis - spaceOnBottom; + + // Scales + const yScale = useMemo(() => + scaleBand({ + domain: data.map((d) => d.label), + range: [0, yMax], + padding: 0.2, + }), [data, yMax]) + + const xScale = useMemo(() => + scaleLinear({ + domain: [0, Math.max(...data.map((d) => d.value))], + range: [0, Math.max(xMax, 0)], + }), [data, xMax]) + + return ( +
+ {data.length === 0 ? +

No Data To Display

+ : + + + {/* Top Axis with Label */} + + {data.map((d) => { + const barHeight = yScale.bandwidth(); + const barWidth = xScale(d.value) ?? 0; + const barY = yScale(d.label); + const barX = 0; + return ( + onBarClicked && onBarClicked(d)} + style={onBarClicked && { cursor: 'pointer' }} + onMouseMove={(event) => handleMouseMove(event, d)} + onMouseLeave={() => hideTooltip()} + > + {/* Category label to the left of each bar */} + + {d.category} + + + + {/* Value label next to the bar */} + + {d.label} + + + + ); + })} + + + + } + {/* Maybe should provide a default tooltip */} + {TooltipContents && tooltipOpen && ( + + + + + + )} +
+ ); +}; + +export default VerticalBarPlot; diff --git a/screen2.0/src/app/applets/gene-expression/MultiSelect.tsx b/screen2.0/src/app/applets/gene-expression/MultiSelect.tsx new file mode 100644 index 00000000..54b19ed7 --- /dev/null +++ b/screen2.0/src/app/applets/gene-expression/MultiSelect.tsx @@ -0,0 +1,155 @@ +import * as React from 'react'; +import Checkbox from '@mui/material/Checkbox'; +import TextField from '@mui/material/TextField'; +import Autocomplete, { AutocompleteChangeDetails, AutocompleteChangeReason } from '@mui/material/Autocomplete'; +import CheckBoxOutlineBlankIcon from '@mui/icons-material/CheckBoxOutlineBlank'; +import CheckBoxIcon from '@mui/icons-material/CheckBox'; +import { Box, Divider, FormControlLabel, Paper } from '@mui/material'; + +function capitalizeWords(input: string): string { + return input.replace(/\b\w/g, char => char.toUpperCase()); +} + +const icon = ; +const checkedIcon = ; + +export type MultiSelectOnChange = (event: React.SyntheticEvent, value: string[], reason: AutocompleteChangeReason, details?: AutocompleteChangeDetails) => void + +export interface MultiSelectProps { + onChange?: MultiSelectOnChange, + options: string[], + placeholder: string + limitTags?: number + //todo add width here +} + +const MultiSelect = ({ + onChange, + options, + placeholder, + limitTags +}: MultiSelectProps) => { + const [value, setValue] = React.useState(options); + const scrollRef = React.useRef(0) //needed to preserve the scroll position of the ListBox. Overriding PaperComponent changes the way that the Listbox renders and resets scroll on interaction + + //reset value when options changes + React.useEffect(() => { + setValue(options) + }, [options]) + + const handleChange: MultiSelectOnChange = React.useCallback((event, value, reason, details?) => { + setValue(value) + if (onChange) onChange(event, value, reason, details) + }, [onChange]) + + const handleToggleSelectAll = React.useCallback((event: React.MouseEvent, checked: boolean) => { + const checkedOptions = options.filter(x => value.includes(x)) + const uncheckedOptions = options.filter(x => !value.includes(x)) + if (checked) { + handleChange(event, options, "selectOption", { option: uncheckedOptions }) + } else { + handleChange(event, [], "removeOption", { option: checkedOptions }) + } + }, [handleChange, options, value]) + + // A warning forced usage of React.forwardRef here, even though the ref is not used + const ListboxComponent = React.forwardRef(function ListboxComponent( + listboxProps: React.HTMLAttributes, + ref: React.ForwardedRef + ) { + const { children, ...props } = listboxProps; + const listboxScrollRef = React.useRef(null) + + //use saved scroll value on initial load. For some reason overriding PaperComponent broke the scroll behavior + React.useEffect(() => { + const current = listboxScrollRef.current; + if (current) { + current.scrollTop = scrollRef.current + } + }, []); + + const handleScroll = (event: React.UIEvent) => { + scrollRef.current = event.currentTarget.scrollTop + } + + // Merged ref function to set both refs + const setRefs = (element: HTMLUListElement | null) => { + if (typeof ref === 'function') { + ref(element); // Set the forwarded ref as a function + } else if (ref) { + ref.current = element; // Set the forwarded ref if it's an object + } + listboxScrollRef.current = element; // Set the internal scroll ref + }; + + return ( +
    + {children} +
+ ) + }) + + return ( + ( + + )} + //Immediate child of popper + PaperComponent={(paperProps) => ( + + e.preventDefault()} //prevents closing popper + onClick={(event) => handleToggleSelectAll(event, value.length === options.length ? false : true)} + pl={1.5} + py={0.5} + > + + } + /> + + + {paperProps.children} + + )} + //Parent element of options contained within above {paperProps.children} + ListboxComponent={ListboxComponent} + //Each option + renderOption={(props, option: string, { selected }) => { + const { key, ...optionProps } = props; + return ( +
  • + + {capitalizeWords(option)} +
  • + ); + }} + /> + ); +} + +export default MultiSelect \ No newline at end of file diff --git a/screen2.0/src/app/applets/gene-expression/const.ts b/screen2.0/src/app/applets/gene-expression/const.ts index c5b9bae7..eab42a2e 100644 --- a/screen2.0/src/app/applets/gene-expression/const.ts +++ b/screen2.0/src/app/applets/gene-expression/const.ts @@ -1,2 +1,51 @@ -export const GeneExpressionInfoTooltip = - "This bar plot displays the expression level of a given gene across available cell types and tissues derived from RNA-seq data. By default, the data displayed is log2(TPM + 0.01), but this may be customized by selecting from the data dropdown; FPKM values are also available and the log scale may be turned off. TPM and RPKM are two metrics of gene expression levels and they differ slightly in their approaches to normalizing for sequencing depth and gene length. The sort order dropdown allows sorting of the data by TPM or FPKM and also allows grouping of the expression values by tissue. Mousing over the bars displays more information about the expriments that produced the data points, and clicking on a bar redirects to the corresponging experiment at the ENCODE portal." +export const humanTissues = [ + "adipose", + "adrenal gland", + "blood", + "blood vessel", + "bone", + "brain", + "breast", + "connective tissue", + "embryo", + "epithelium", + "esophagus", + "gallbladder", + "heart", + "kidney", + "large intestine", + "liver", + "lung", + "muscle", + "nerve", + "ovary", + "pancreas", + "penis", + "placenta", + "prostate", + "skin", + "small intestine", + "spleen", + "stomach", + "testis", + "thyroid", + "uterus", + "vagina" +] + +export const mouseTissues = [ + "adrenal gland", + "blood", + "brain", + "embryo", + "epithelium", + "heart", + "intestine", + "kidney", + "limb", + "liver", + "lung", + "muscle", + "stomach", + "thymus" +] diff --git a/screen2.0/src/app/applets/gene-expression/geneexpression.tsx b/screen2.0/src/app/applets/gene-expression/geneexpression.tsx new file mode 100644 index 00000000..a2396a84 --- /dev/null +++ b/screen2.0/src/app/applets/gene-expression/geneexpression.tsx @@ -0,0 +1,574 @@ +"use client" +import React, { useCallback, useMemo, useRef, useState } from "react" +import { LoadingMessage } from "../../../common/lib/utility" +import { useQuery } from "@apollo/client" +import { Button, Typography, Stack, MenuItem, FormControl, InputLabel, OutlinedInput, Select, ToggleButton, ToggleButtonGroup, FormLabel, Tooltip, IconButton, Divider } from "@mui/material" +import Grid from "@mui/material/Grid2" +import Image from "next/image" +import { humanTissues, mouseTissues } from "./const" +import { GENE_EXP_QUERY, GENE_QUERY, GET_ORTHOLOG, GET_ORTHOLOG_DATA, GET_ORTHOLOG_VARS } from "./queries" +import { ReadonlyURLSearchParams, usePathname, useSearchParams, useRouter } from "next/navigation" +import ConfigureGBModal from "../../search/_ccredetails/configuregbmodal" +import { GeneAutocomplete } from "../../search/_geneAutocomplete/GeneAutocomplete" +import { GeneInfo } from "../../search/_geneAutocomplete/types" +import { Close, Download, OpenInNew, Search, SyncAlt } from "@mui/icons-material" +import { LoadingButton } from "@mui/lab" +import DownloadDialog, { FileOption } from "../gwas/_lollipop-plot/DownloadDialog" +import { capitalizeFirstLetter, downloadObjArrayAsTSV, downloadSVG, downloadSvgAsPng } from "../gwas/helpers" +import VerticalBarPlot, { BarData } from "./BarPlot" +import { tissueColors } from "../../../common/lib/colors" +import MultiSelect, { MultiSelectOnChange } from "./MultiSelect" + +const biosampleTypes = ["cell line", "primary cell", "tissue", "in vitro differentiated cells" ]; + +type Assembly = "GRCh38" | "mm10" + +const initialTissues = (assembly: Assembly) => { + if (assembly === "GRCh38") { + return humanTissues + } else { + return mouseTissues + } +} + +//extracted from generated types, needed the nested type to pass as type argument to BarData +type GeneDataset = { __typename?: 'GeneDataset', biosample: string, tissue?: string | null, cell_compartment?: string | null, biosample_type?: string | null, assay_term_name?: string | null, accession: string, gene_quantification_files?: Array<{ __typename?: 'GeneQuantificationFile', accession: string, biorep?: number | null, quantifications?: Array<{ __typename?: 'GeneQuantification', tpm: number, file_accession: string } | null> | null } | null> | null } + +export function GeneExpression(props: { + assembly: Assembly + genes?: { name: string, linkedBy?: string[] }[] + applet?: boolean +}) { + const searchParams: ReadonlyURLSearchParams = useSearchParams() + const urlAssembly = searchParams.get("assembly") + const initialAssembly = ((urlAssembly === "GRCh38") || (urlAssembly === "mm10")) ? urlAssembly : props.assembly + const urlGene = searchParams.get("gene") + const router = useRouter() + const pathname = usePathname() + + //If genes passed as prop, use those. This is case in cCRE Details. Else use url gene if passed, default to APOE + const [gene, setGene] = useState(props.genes ? props?.genes[0]?.name : (urlGene ?? "APOE")) + const [assembly, setAssembly] = useState(initialAssembly) + const [biosamples, setBiosamples] = useState(biosampleTypes) + const [tissues, setTissues] = useState(() => initialTissues(initialAssembly)) + const [viewBy, setViewBy] = useState<"byTissueMaxTPM" | "byExperimentTPM" | "byTissueTPM">("byExperimentTPM") + const [RNAtype, setRNAType] = useState<"all" | "polyA plus RNA-seq" | "total RNA-seq">("total RNA-seq") + const [scale, setScale] = useState<"linearTPM" | "logTPM">("linearTPM") + const [replicates, setReplicates] = useState<"mean" | "all">("mean") + const [configGBopen, setConfigGBOpen] = useState(false); + const [downloadOpen, setDownloadOpen] = useState(false) + const [search, setSearch] = useState("") + + const plotRef = useRef() + + const handleOpenConfigGB = () => { + if (gene) setConfigGBOpen(true) + } + + const handleSetSearch = (event: React.ChangeEvent) => { + setSearch(event.target.value) + }; + + const sampleMatchesSearch = useCallback((x: GeneDataset): boolean => { + if (search) { + return x.accession.toLowerCase().includes(search.toLowerCase()) + || x.biosample.toLowerCase().includes(search.toLowerCase()) + || x.tissue.toLowerCase().includes(search.toLowerCase()) + || !!x.gene_quantification_files.map(x => x.accession).find(y => y.toLowerCase().includes(search.toLowerCase())) + } else return true + }, [search]) + + //Fetch Gene info to get ID + //This query seems like it shouldn't be necessary, but ID needed in second query + //and component isn't setup to take in ID as prop so leaving as-is. -Jonathan 7/25/24 + //Gene autocomplete exposes ID, which makes this avoidable aside from initial load. + const { + data: dataGeneID, + loading: loadingGeneID + } = useQuery(GENE_QUERY, { + variables: { + assembly: assembly.toLowerCase(), + name: [gene], + version: assembly === "GRCh38" ? 40 : 25 + }, + skip: !gene, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + }) + + //Fetch Gene Exp data + const { + data: dataExperiments, + loading: loadingExperiments + } = useQuery(GENE_EXP_QUERY, { + variables: { + assembly: assembly, + gene_id: dataGeneID && dataGeneID.gene.length > 0 && dataGeneID.gene[0].id.split(".")[0] + }, + skip: !gene || !dataGeneID || (dataGeneID && dataGeneID.gene.length === 0), + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + }) + + const { data: dataOrtholog, loading: loadingOrtholog, error: errorOrtholog } = useQuery(GET_ORTHOLOG, { + variables: { + name: [gene], + assembly: assembly.toLowerCase() as "mm10" | "grch38" + }, + skip: !gene + }) + + const makeLabel = (tpm: number, biosample: string, accession: string, biorep?: number): string => { + return `${tpm.toFixed(2)}, ${biosample.length > 25 ? biosample.slice(0, 23) + '...' : biosample} (${accession}${biorep ? ', rep. ' + biorep : ''})` + } + + const scaleData = useCallback((value: number) => { + switch (scale) { + case ("linearTPM"): return value; + case ("logTPM"): return Math.log10(value + 1) + } + }, [scale]) + + + const plotData: BarData[] = useMemo(() => { + if (dataExperiments && dataExperiments.gene_dataset.length > 0) { + //Filter data points + const filteredData = dataExperiments.gene_dataset + .filter(d => biosamples.includes(d.biosample_type)) //biosample type + .filter(d => tissues.includes(d.tissue)) //tissue + .filter(d => RNAtype === "all" || d.assay_term_name === RNAtype) //RNA type + .filter(d => sampleMatchesSearch(d)) //search + //holder for plot data as replicates are parsed for each experiment + let parsedReplicates: BarData[] = [] + filteredData.forEach((biosample) => { + if (replicates === "all") { //push all replicates + biosample.gene_quantification_files.forEach((exp) => { + parsedReplicates.push({ + category: biosample.tissue, + label: makeLabel(scaleData(exp.quantifications[0].tpm), biosample.biosample, biosample.accession, exp.biorep), + value: scaleData(exp.quantifications[0].tpm), //indexing into 0th position, only one gene so quantifications should always be length 1 + color: tissueColors[biosample.tissue] ?? tissueColors.missing, + metadata: biosample as GeneDataset + }) + }) + } else { //average replicates + let sum = 0 + biosample.gene_quantification_files.forEach((exp) => { + sum += (exp.quantifications[0].tpm) //using reduce had terrible readability so doing avg manually + }) + const avgTPM = sum / biosample.gene_quantification_files.length + parsedReplicates.push({ + category: biosample.tissue, + label: makeLabel(scaleData(avgTPM), biosample.biosample, biosample.accession), //omit biorep + value: scaleData(avgTPM), + color: tissueColors[biosample.tissue] ?? tissueColors.missing, + metadata: biosample as GeneDataset + }) + } + }) + switch (viewBy) { + case ("byExperimentTPM"):{ + //sort by value + parsedReplicates.sort((a, b) => b.value - a.value); + break; + } + case ("byTissueTPM"): { + //find max value for each tissue + const maxValuesByTissue: {[key: string]: number} = parsedReplicates.reduce((acc, item) => { + acc[item.category] = Math.max(acc[item.category] || -Infinity, item.value); + return acc; + }, {}); + + //sort by max value for tissue, and sort within the tissue itself + parsedReplicates.sort((a, b) => { + const maxDiff = maxValuesByTissue[b.category] - maxValuesByTissue[a.category]; + return maxDiff !== 0 ? maxDiff : b.value - a.value; + }); + break; + } + case ("byTissueMaxTPM"): { + //find max value for each tissue + const maxValuesByTissue: {[key: string]: number} = parsedReplicates.reduce((acc, item) => { + acc[item.category] = Math.max(acc[item.category] || -Infinity, item.value); + return acc; + }, {}); + + //filter out all but max value for each tissue, then sort descending + parsedReplicates = parsedReplicates.filter(x => x.value === maxValuesByTissue[x.category]) + parsedReplicates.sort((a, b) => b.value - a.value); + } + } + return parsedReplicates + } else return [] + }, [RNAtype, biosamples, dataExperiments, replicates, sampleMatchesSearch, scaleData, tissues, viewBy]) + + const handleSetAssembly = (newAssembly: Assembly) => { + if (props.applet) { //only allow switch in applet. Check should never fail but keeping + setAssembly(newAssembly) + if (newAssembly === "GRCh38") { + setTissues(humanTissues) //Reset Tissue Filter + setRNAType("total RNA-seq") //Switch back RNA type if going from mouse to human, as all data there is total + } else { + setTissues(mouseTissues) //Reset Tissue Filter + } + } + } + + const handleGroupChange = ( + event: React.MouseEvent, + newView: string | null, + ) => { + if ((newView !== null) && ((newView === "byTissueMaxTPM") || (newView === "byExperimentTPM") || (newView === "byTissueTPM"))) { + setViewBy(newView) + } + }; + + const handleRNATypeChange = ( + event: React.MouseEvent, + newRNA: string | null, + ) => { + if ((newRNA !== null) && ((newRNA === "all") || (newRNA === "polyA plus RNA-seq") || (newRNA === "total RNA-seq"))) { + setRNAType(newRNA) + } + }; + + const handleScaleChange = ( + event: React.MouseEvent, + newScale: string | null, + ) => { + if ((newScale !== null) && ((newScale === "linearTPM") || (newScale === "logTPM"))) { + setScale(newScale) + } + }; + + const handleReplicatesChange = ( + event: React.MouseEvent, + newReplicates: string | null, + ) => { + if ((newReplicates !== null) && ((newReplicates === "mean") || (newReplicates === "all"))) { + setReplicates(newReplicates) + } + }; + + const handleDownload = useCallback((selectedOptions: FileOption[]) => { + if (selectedOptions.includes('svg')) { downloadSVG(plotRef, gene + '_gene_expression') } + if (selectedOptions.includes('png')) { downloadSvgAsPng(plotRef, gene + '_gene_expression') } + if (selectedOptions.includes('tsv')) { + const toDownload: { accession: string, biosample: string, tissue: string, tpm: string }[] = [...dataExperiments.gene_dataset] + .map(x => { + return { + accession: x.accession, + biosample: x.biosample, + tissue: x.tissue, + tpm: (x.gene_quantification_files.reduce((acc, cur) => acc + cur.quantifications?.[0]?.tpm, 0) / x.gene_quantification_files.length).toFixed(2) + } + }) + .sort((a, b) => a.accession.localeCompare(b.accession)) + downloadObjArrayAsTSV(toDownload, gene + '_gene_expression') + } + }, [dataExperiments?.gene_dataset, gene]) + + const PlotTooltip = useCallback((bar: BarData) => { + return ( + <> + Clicking opens this experiment on ENCODE +
    + Accession: {bar.metadata.accession} + Sample: {capitalizeFirstLetter(bar.metadata.biosample)} + Tissue: {capitalizeFirstLetter(bar.metadata.tissue)} + Biosample Type: {capitalizeFirstLetter(bar.metadata.biosample_type)} + {scale === "linearTPM" ? + TPM: {bar.value} + : + Log10(TPM + 1): {bar.value} + } + + ) + }, [scale]) + + const handleSetTissues: MultiSelectOnChange = (_, value) => { + setTissues(value) + } + + const handleSetBiosamples: MultiSelectOnChange = (_, value) => { + setBiosamples(value) + } + + const handleSetGene = (newGene: string) => { + setGene(newGene) + } + + return ( + + + + Gene Expression Profiles by RNA-seq + + + + + + + {props.applet ? + + + { + handleSetGene(gene ? gene.name : null) + router.push(`${pathname}?assembly=${assembly}&gene=${gene ? gene.name : ''}`) + }} + onGeneSubmitted={(gene: GeneInfo) => { + handleSetGene(gene ? gene.name : null) + router.push(`${pathname}?assembly=${assembly}&gene=${gene ? gene.name : ''}`) + }} + /> + } + onClick={() => { + const newGene = dataOrtholog.geneOrthologQuery[0][assembly === "GRCh38" ? 'mouseGene' : 'humanGene'] + const newAssembly = assembly === "GRCh38" ? "mm10" : "GRCh38" + handleSetGene(newGene) + handleSetAssembly(newAssembly) + router.push(`${pathname}?assembly=${newAssembly}&gene=${newGene}`) + }} + > + {dataOrtholog?.geneOrthologQuery.length > 0 ? + <> + {`Go to ${assembly === "GRCh38" ? "mm10" : "GRCh38"} ortholog:`} {dataOrtholog?.geneOrthologQuery[0][assembly === "GRCh38" ? 'mouseGene' : 'humanGene']} + + : + `No ortholog found in ${assembly === "GRCh38" ? "mm10" : "GRCh38"}` + } + + + : + + Gene + + + } + {/* Plot controls/filters */} + + + RNA-seq Type + + {/* Human only has total RNA-seq, so disable other options when in human */} + Total + +
    {/** div needed to show tooltip when button disabled */} + PolyA+ +
    +
    + +
    + All +
    +
    +
    +
    + + Scale + + Linear TPM + Log10(TPM + 1) + + + + View By + + Experiment + Tissue + Tissue Max + + + + Replicates + + Average + Show Replicates + + + + {biosamples.length === biosampleTypes.length ? "Biosample Types" : Biosample Types*} + + + + {tissues.length === initialTissues(assembly).length ? "Tissues" : Tissues*} + + +
    + + + + Search Samples + setSearch("")}> : } + label="Search Samples" + placeholder="ID, Tissue, Biosample" + value={search} + onChange={handleSetSearch} /> + + + + + + { + loadingGeneID || loadingExperiments ? + + + + : + dataExperiments ? + + window.open("https://www.encodeproject.org/experiments/" + x.metadata.accession, "_blank", "noopener,noreferrer")} + TooltipContents={(bar) => } + /> + + : + + Please Select a Gene + + } + {/* Configure Trackhub */} + + {/* Download Dialog */} + setDownloadOpen(false)} + onSubmit={handleDownload} + /> +
    + ); +} diff --git a/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx b/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx deleted file mode 100644 index e585e465..00000000 --- a/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx +++ /dev/null @@ -1,221 +0,0 @@ -import React from "react" -import { useRouter } from "next/navigation" -import { Stack } from "@mui/material" -import { Range2D, Point2D, linearTransform2D } from "jubilant-carnival" -import { tissueColors } from "../../../common/lib/colors" - -type QuantificationData = { - accession: string, - assay_term_name: string, - biosample: string, - biosample_type: string, - color: string, - file_accession: string, - tpm: number, - value: number, - replicate_num: number, -}[] - -/** - * @todo Need to type everything in this file and clean it up. It's very confusing - */ - -export function PlotGeneExpression(props: { - data: { - accession: string, - assay_term_name: string, - biosample: string, - biosample_type: string, - cell_compartment: string, - gene_quantification_files: { accession: string, biorep: number, quantifications: { file_accession: string, tpm: number }[] }[], - tissue: string - }[] - range: Range2D - dimensions: Range2D - // RNAtype: string - group: "byTissueMaxTPM" | "byExperimentTPM" | "byTissueTPM" - scale: "linearTPM" | "logTPM" - replicates: "mean" | "all" -}) { - const router = useRouter() - - let byTissue: { [id: string]: { values: QuantificationData } } = {} - let byTissueMean: { [id: string]: { values: QuantificationData } } = {} - let byValueTissues: { [id: string]: { values: QuantificationData } } = {} - let byTissueMax: { [id: string]: { values: QuantificationData } } = {} - let p1: Point2D = { x: 0, y: 0 } - //Holds the max value in the chart - let max: number = 0 - - //Iterate through each biosample, and group by tissue type - props.data.filter(s => s["tissue"]).map((biosample) => { - - if (!byTissue[biosample["tissue"]]) { - byTissue[biosample["tissue"]] = { values: [] } - } - - biosample["gene_quantification_files"].forEach((file, i) => { - if (file.quantifications.length > 0) { - file.quantifications.forEach(q => { - let val = props.scale === "logTPM" ? Math.log10(q.tpm + 1) : q.tpm - if (val > max) { - max = val - } - if (q.tpm > 0) { - byTissue[biosample["tissue"]].values.push({ - biosample: biosample.biosample, - biosample_type: biosample.biosample_type, - assay_term_name: biosample.assay_term_name, - accession: biosample.accession, - value: val, tpm: q.tpm, file_accession: q.file_accession, - color: tissueColors[biosample["tissue"]] ?? tissueColors.missing, - replicate_num: file.biorep - }) - } - }) - } - }) - }) - - if (props.replicates === "mean") { - Object.keys(byTissue).forEach(k => { - if (!byTissueMean[k]) byTissueMean[k] = { values: [] } - let datasetAccessions = [...new Set(byTissue[k].values.map(v => v.accession))]; - - datasetAccessions.forEach(da => { - let r = byTissue[k].values.filter(v => v.accession == da) - let sum = r.map(v => v.value).reduce((partialSum, a) => partialSum + a, 0); - byTissueMean[k].values.push( - { - biosample: r[0].biosample, - biosample_type: r[0].biosample_type, - assay_term_name: r[0].assay_term_name, - accession: r[0].accession, - value: sum / r.length, - tpm: r[0].tpm, - file_accession: r[0].file_accession, - color: tissueColors[k] ?? tissueColors.missing, - replicate_num: 0 - } - ) - }) - }) - byTissue = byTissueMean - } - - //Sort descending within each tissue group, eliminate any tissues that are empty. Push max value to byTissueMax - Object.keys(byTissue).forEach(tissue => { - if (byTissue[tissue].values.length === 0) { - delete byTissue[tissue]; //eliminate tissue if empty - } else { - byTissue[tissue].values.sort((a, b) => b.value - a.value) //sort descending - byTissueMax[tissue] = { - values: [byTissue[tissue].values[0]] //extract max value to put in byTissueMax - } - } - }) - - props.range.x.end = max - - // returns bar plot for a tissue - const plotGeneExp = (entry, _, y) => { - - let info = entry[1] - - return info.values.map((item: { color: string, biosample: string, file_accession: string, accession: string, value: number, replicate_num: number }, i: number) => { - //Shouldn't this just be LinearTransform? Why 2D? - p1 = linearTransform2D(props.range, props.dimensions)({ x: Number(item.value.toFixed(2)), y: 0 }) - return ( - - {/* The color bar */} - - - {item.value.toFixed(2) + "\n" + item.biosample + "\n" + item.accession + "-" + item.file_accession + "\n" + "Clicking opens this experiment in a new tab"} - - - - {/* The score and exp/biosample ID */} - - {item.value.toFixed(2) + ", "} - {item.biosample + " ("} - {item.accession} - {item.replicate_num ? ", rep. " + item.replicate_num + ")" : ")"} - - - - {/* The biosample category */} - {(props.group === 'byTissueMaxTPM' || props.group === 'byExperimentTPM') && - - {entry[0].split("-")[0]} - - } - {props.group === 'byTissueTPM' && i === Math.floor(Object.values(info.values).length / 2) && - - {entry[0].split("-")[0]} - - } - - - ) - }) - } - - let byValuesTissues = Object.entries(byTissue).map((entry) => { - let info = entry[1] - return info.values.map(r => { - return { - ...r, - tissue: entry[0] - } - }) - }).flat() - let byValTissues = (byValuesTissues.sort((a, b) => b.value - a.value)) - - byValTissues.forEach((b, i) => { - byValueTissues[b.tissue + "-b" + i] = { values: [b] } - }) - - - - - let tissues: { [id: string]: { values: QuantificationData } } = props.group === "byExperimentTPM" ? byValueTissues : props.group === "byTissueMaxTPM" ? byTissueMax : byTissue // dict of ftissues - - const sortedTissues = Object.fromEntries( - Object.entries(tissues).sort((tissueA, tissueB) => Math.max(...tissueB[1].values.map(x => x.value)) - Math.max(...tissueA[1].values.map(x => x.value))) - ); - - return ( - Object.keys(sortedTissues).length === 0 ? - {'No Data Available'} - : - - {Object.entries(sortedTissues).map((entry, index: number) => { - let info = entry[1] - let view: string = "0 0 1200 " + (info.values.length * (props.group === 'byTissueTPM' ? 20 : 3) + 20) - return ( - - - {/* Why 5? */} - {plotGeneExp(entry, index, 5)} - - - ) - })} - - ) -} diff --git a/screen2.0/src/app/applets/gene-expression/page.tsx b/screen2.0/src/app/applets/gene-expression/page.tsx index 8298a776..e31fcfd1 100644 --- a/screen2.0/src/app/applets/gene-expression/page.tsx +++ b/screen2.0/src/app/applets/gene-expression/page.tsx @@ -1,6 +1,6 @@ "use client" import { Box } from "@mui/material" -import { GeneExpression } from "../../search/_ccredetails/geneexpression" +import { GeneExpression } from "./geneexpression" import { Suspense } from "react" diff --git a/screen2.0/src/app/applets/gene-expression/queries.ts b/screen2.0/src/app/applets/gene-expression/queries.ts index a23b3102..a08b0281 100644 --- a/screen2.0/src/app/applets/gene-expression/queries.ts +++ b/screen2.0/src/app/applets/gene-expression/queries.ts @@ -1,5 +1,6 @@ -import { gql } from "@apollo/client" -export const GENE_EXP_QUERY = gql` +import { gql } from "../../../graphql/__generated__/gql" + +export const GENE_EXP_QUERY = gql(` query geneexpression($assembly: String!, $gene_id: [String]) { gene_dataset(processed_assembly: $assembly) { biosample @@ -14,13 +15,12 @@ query geneexpression($assembly: String!, $gene_id: [String]) { quantifications(gene_id_prefix: $gene_id) { tpm file_accession - fpkm } } } } - ` -export const GENE_QUERY = gql` + `) +export const GENE_QUERY = gql(` query geneAutocomplete($assembly: String!, $name: [String!], $limit: Int, $version: Int) { gene(assembly: $assembly, name: $name, limit: $limit, version: $version) { name @@ -31,7 +31,7 @@ export const GENE_QUERY = gql` end } } - } ` + } ` ) export type GET_ORTHOLOG_VARS = { name: string[], @@ -45,11 +45,11 @@ export type GET_ORTHOLOG_DATA = { }[] } -export const GET_ORTHOLOG = gql` +export const GET_ORTHOLOG = gql(` query geneOrthologQuery($name: [String]!, $assembly: String!) { geneOrthologQuery: geneorthologQuery(name: $name, assembly: $assembly) { humanGene: external_gene_name mouseGene: mmusculus_homolog_associated_gene_name } } -` \ No newline at end of file +`) \ No newline at end of file diff --git a/screen2.0/src/app/applets/gwas/_lollipop-plot/DownloadDialog.tsx b/screen2.0/src/app/applets/gwas/_lollipop-plot/DownloadDialog.tsx index afd18217..e9e0374c 100644 --- a/screen2.0/src/app/applets/gwas/_lollipop-plot/DownloadDialog.tsx +++ b/screen2.0/src/app/applets/gwas/_lollipop-plot/DownloadDialog.tsx @@ -8,16 +8,22 @@ import Checkbox from '@mui/material/Checkbox'; import FormControlLabel from '@mui/material/FormControlLabel'; import { Divider, Stack, Typography } from '@mui/material'; -interface DownloadDialogProps { +/** + * @todo This component is being referrenced by gene expression plot also, maybe move this + */ + +interface DownloadDialogProps { open: boolean; + fileFormats: T + defaultSelected: Array onClose: () => void; - onSubmit: (selections: string[]) => void; + onSubmit: (selections: Array) => void; } export type FileOption = 'png' | 'svg' | 'tsv' | 'json' -const DownloadDialog: React.FC = ({ open, onClose, onSubmit }) => { - const [selectedOptions, setSelectedOptions] = React.useState(['png']); +const DownloadDialog = ({ open, fileFormats, defaultSelected, onClose, onSubmit }: DownloadDialogProps) => { + const [selectedOptions, setSelectedOptions] = React.useState(defaultSelected); const handleToggle = (value: string) => { const currentIndex = selectedOptions.indexOf(value as FileOption); @@ -43,22 +49,22 @@ const DownloadDialog: React.FC = ({ open, onClose, onSubmit Select format for download - handleToggle('png')} />} label="Plot (.png)" - /> - } + {fileFormats.includes('svg') && handleToggle('svg')} />} label="Plot (.svg)" - /> - } + {fileFormats.includes('tsv') && handleToggle('tsv')} />} label="Data (.tsv)" - /> - } + {fileFormats.includes('json') && handleToggle('json')} />} label="Data (.json)" - /> + />} diff --git a/screen2.0/src/app/applets/gwas/_lollipop-plot/lollipopplot.tsx b/screen2.0/src/app/applets/gwas/_lollipop-plot/lollipopplot.tsx index a8f307fb..163b452b 100644 --- a/screen2.0/src/app/applets/gwas/_lollipop-plot/lollipopplot.tsx +++ b/screen2.0/src/app/applets/gwas/_lollipop-plot/lollipopplot.tsx @@ -518,6 +518,8 @@ export const EnrichmentLollipopPlot = (props: EnrichmentLollipopPlot) => { )} setDownloadOpen(false)} onSubmit={handleDownload} /> diff --git a/screen2.0/src/app/applets/gwas/helpers.ts b/screen2.0/src/app/applets/gwas/helpers.ts index 77e38d29..9569d26d 100644 --- a/screen2.0/src/app/applets/gwas/helpers.ts +++ b/screen2.0/src/app/applets/gwas/helpers.ts @@ -6,13 +6,16 @@ export const capitalizeFirstLetter = (string) => { * Downloads .svg from given SVG ref * * @param ref ref passed to parent svg container - * @param filename + * @param filename prefix (.svg added) * * @info Taken straight from ChatGPT, use with caution * */ export const downloadSVG = (ref: React.MutableRefObject, filename: string) => { - if (!ref.current) return; + if (!ref.current) { + console.error('SVG reference is not set.'); + return; + } const serializer = new XMLSerializer(); const source = serializer.serializeToString(ref.current); @@ -30,7 +33,7 @@ export const downloadSVG = (ref: React.MutableRefObject, filename * Downloads .png from given SVG ref * * @param ref ref passed to parent svg container - * @param filename + * @param filename prefix (.png added) * * @info Mostly taken straight from ChatGPT, use with caution * @@ -95,7 +98,7 @@ export const downloadSvgAsPng = (ref: React.MutableRefObject, fil /** * * @param exportObj - * @param filename + * @param filename prefix (.json added) * * @info Taken straight from ChatGPT, use with caution */ @@ -112,7 +115,7 @@ export const downloadObjectAsJson = (exportObj: {[key: string]: any}, filename: /** * * @param exportArr - * @param filename + * @param filename prefix (.tsv added) * * @info Taken straight from ChatGPT, use with caution */ diff --git a/screen2.0/src/app/search/_ccredetails/ccredetails.tsx b/screen2.0/src/app/search/_ccredetails/ccredetails.tsx index 161ce95a..0363e445 100644 --- a/screen2.0/src/app/search/_ccredetails/ccredetails.tsx +++ b/screen2.0/src/app/search/_ccredetails/ccredetails.tsx @@ -11,7 +11,7 @@ import { FunctionData } from "./functionaldata" import { ChromHMM } from "./chromhmm"; import { ENTExData } from "./entexdata"; import Rampage from "./rampage" -import { GeneExpression } from "./geneexpression" +import { GeneExpression } from "../../applets/gene-expression/geneexpression" import { TfSequenceFeatures } from "../_gbview/tfsequencefeatures" import ConfigureGBTab from "./configuregbtab" import { useQuery } from "@apollo/client" diff --git a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx deleted file mode 100644 index 5aaff693..00000000 --- a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx +++ /dev/null @@ -1,432 +0,0 @@ -"use client" -import React, { useMemo, useState } from "react" -import { LoadingMessage } from "../../../common/lib/utility" -import { PlotGeneExpression } from "../../applets/gene-expression/geneexpressionplot" -import { useQuery } from "@apollo/client" -import { Button, Typography, Stack, MenuItem, FormControl, SelectChangeEvent, Checkbox, InputLabel, ListItemText, OutlinedInput, Select, ToggleButton, ToggleButtonGroup, FormLabel, Box } from "@mui/material" -import Grid from "@mui/material/Grid2" -import Image from "next/image" -import { GENE_EXP_QUERY, GENE_QUERY, GET_ORTHOLOG, GET_ORTHOLOG_DATA, GET_ORTHOLOG_VARS } from "../../applets/gene-expression/queries" -import { ReadonlyURLSearchParams, usePathname, useSearchParams, useRouter } from "next/navigation" -import ConfigureGBModal from "./configuregbmodal" -import { GeneAutocomplete } from "../_geneAutocomplete/GeneAutocomplete" -import { GeneInfo } from "../_geneAutocomplete/types" -import { SyncAlt } from "@mui/icons-material" -import { LoadingButton } from "@mui/lab" - -/** - * @todo - * Download - * Tooltip with correct info - * - */ - -const ITEM_HEIGHT = 48; -const ITEM_PADDING_TOP = 8; -const MenuProps = { - PaperProps: { - style: { - maxHeight: ITEM_HEIGHT * 8.5 + ITEM_PADDING_TOP, - width: 200, - }, - }, -}; - -const biosampleTypes = ["cell line", "in vitro differentiated cells", "primary cell", "tissue"]; - -type Assembly = "GRCh38" | "mm10" - -export function GeneExpression(props: { - assembly: Assembly - genes?: { name: string, linkedBy?: string[] }[] - applet?: boolean -}) { - const searchParams: ReadonlyURLSearchParams = useSearchParams() - const urlAssembly = searchParams.get("assembly") - const urlGene = searchParams.get("gene") - const router = useRouter() - const pathname = usePathname() - - //If genes passed as prop, use those. This is case in cCRE Details. Else use url gene if passed, default to APOE - const [gene, setGene] = useState(props.genes ? props?.genes[0]?.name : (urlGene ?? "APOE")) - const [dataAssembly, setDataAssembly] = useState(((urlAssembly === "GRCh38") || (urlAssembly === "mm10")) ? urlAssembly : props.assembly) - const [searchAssembly, setSearchAssembly] = useState(((urlAssembly === "GRCh38") || (urlAssembly === "mm10")) ? urlAssembly : props.assembly) - - const [biosamples, setBiosamples] = useState(["cell line", "in vitro differentiated cells", "primary cell", "tissue"]) - const [group, setGroup] = useState<"byTissueMaxTPM" | "byExperimentTPM" | "byTissueTPM">("byExperimentTPM") - const [RNAtype, setRNAType] = useState<"all" | "polyA plus RNA-seq" | "total RNA-seq">("total RNA-seq") - const [scale, setScale] = useState<"linearTPM" | "logTPM">("linearTPM") - const [replicates, setReplicates] = useState<"mean" | "all">("mean") - const [configGBopen, setConfigGBOpen] = useState(false); - - const handleOpenConfigGB = () => { - // (assembly === "GRCh38" ? dataHumanGene?.gene[0] : dataMouseGene?.gene[0]) && setConfigGBOpen(true) - //Why was the first return data being checked before allowing it to be opened? I get checking to see if the gene state var is set... - gene && setConfigGBOpen(true) - } - - //Fetch Gene info to get ID - //This query seems like it shouldn't be necessary, but ID needed in second query - //and component isn't setup to take in ID as prop so leaving as-is. -Jonathan 7/25/24 - //Gene autocomplete exposes ID, which makes this avoidable aside from initial load. - const { - data: dataGeneID, - loading: loadingGeneID - } = useQuery(GENE_QUERY, { - variables: { - assembly: dataAssembly.toLowerCase(), - name: [gene], - version: dataAssembly === "GRCh38" ? 40 : 25 - }, - skip: !gene, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - }) - - //Fetch Gene Exp data - const { - data: dataExperiments, - loading: loadingExperiments - } = useQuery(GENE_EXP_QUERY, { - variables: { - assembly: dataAssembly, - gene_id: dataGeneID && dataGeneID.gene.length > 0 && dataGeneID.gene[0].id.split(".")[0] - }, - skip: !gene || !dataGeneID || (dataGeneID && dataGeneID.gene.length === 0), - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - }) - - const { data: dataOrtholog, loading: loadingOrtholog, error: errorOrtholog } = useQuery(GET_ORTHOLOG, { - variables: { - name: [gene], - assembly: dataAssembly.toLowerCase() as "mm10" | "grch38" - }, - skip: !gene - }) - - //Generate gene expression data for chart - //Filter it based on biosample types and RNA types selections - const plotGeneExpData = useMemo(() => { - if (dataExperiments && dataExperiments.gene_dataset.length > 0) { - return RNAtype === "all" ? - dataExperiments.gene_dataset - .filter(d => biosamples.includes(d.biosample_type)) - : - dataExperiments.gene_dataset - .filter(d => biosamples.includes(d.biosample_type)) - .filter(r => r.assay_term_name === RNAtype) - } else return [] - }, [RNAtype, biosamples, dataExperiments]) - - //Handle assembly switch for search - const handleSetDataAssembly = (newAssembly: Assembly) => { - if (props.applet) { - setDataAssembly(newAssembly) - //Switch back RNA type if going from mouse to human, as all data there is total - if (dataAssembly === "GRCh38") { - setRNAType("total RNA-seq") - } - } - } - - const handleGroupChange = ( - event: React.MouseEvent, - newView: string | null, - ) => { - if ((newView !== null) && ((newView === "byTissueMaxTPM") || (newView === "byExperimentTPM") || (newView === "byTissueTPM"))) { - setGroup(newView) - } - }; - - const handleRNATypeChange = ( - event: React.MouseEvent, - newRNA: string | null, - ) => { - if ((newRNA !== null) && ((newRNA === "all") || (newRNA === "polyA plus RNA-seq") || (newRNA === "total RNA-seq"))) { - setRNAType(newRNA) - } - }; - - const handleScaleChange = ( - event: React.MouseEvent, - newScale: string | null, - ) => { - if ((newScale !== null) && ((newScale === "linearTPM") || (newScale === "logTPM"))) { - setScale(newScale) - } - }; - - const handleReplicatesChange = ( - event: React.MouseEvent, - newReplicates: string | null, - ) => { - if ((newReplicates !== null) && ((newReplicates === "mean") || (newReplicates === "all"))) { - setReplicates(newReplicates) - } - }; - - const handleBiosampleChange = (event: SelectChangeEvent) => { - const { - target: { value }, - } = event; - setBiosamples( - // On autofill we get a stringified value. - typeof value === 'string' ? value.split(',') : value, - ); - }; - - return ( - - - - Gene Expression Profiles by RNA-seq - - - - - - - {props.applet ? - - - { - setGene(gene ? gene.name : null) - setDataAssembly(searchAssembly) - router.push(`${pathname}?assembly=${searchAssembly}&gene=${gene ? gene.name : ''}`) - }} - onGeneSubmitted={(gene: GeneInfo) => { - setGene(gene ? gene.name : null) - setDataAssembly(searchAssembly) - router.push(`${pathname}?assembly=${searchAssembly}&gene=${gene ? gene.name : ''}`) - }} - /> - } - onClick={() => { - const newGene = dataOrtholog.geneOrthologQuery[0][dataAssembly === "GRCh38" ? 'mouseGene' : 'humanGene'] - const newAssembly = dataAssembly === "GRCh38" ? "mm10" : "GRCh38" - setGene(newGene) - setDataAssembly(newAssembly) - router.push(`${pathname}?assembly=${newAssembly}&gene=${newGene}`) - }} - > - {dataOrtholog?.geneOrthologQuery.length > 0 ? - <> - {`Go to ${dataAssembly === "GRCh38" ? "mm10" : "GRCh38"} ortholog:`} {dataOrtholog?.geneOrthologQuery[0][dataAssembly === "GRCh38" ? 'mouseGene' : 'humanGene']} - - : - `No ortholog found in ${dataAssembly === "GRCh38" ? "mm10" : "GRCh38"}` - } - - - : - - Gene - - - } - - - Biosample Types - - - {/* RNA Type, hide for human as all data is total RNA-seq */} - {dataAssembly === "mm10" && - RNA Type - - Total RNA-seq - PolyA plus RNA-seq - All - - } - - Scale - - Linear TPM - Log10(TPM + 1) - - - - View By - - Experiment - Tissue - Tissue Max - - - - Replicates - - Average Replicates - Individual Replicates - - - - - - - - { - loadingGeneID || loadingExperiments ? - - - - : - dataExperiments ? - - - Gene Expression of {gene} in {dataAssembly}: - - - - : - - Please Select a Gene - - } - {/* Configure Trackhub */} - - - ); -} diff --git a/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx b/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx index 411fd879..3f4ff100 100644 --- a/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx +++ b/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx @@ -1,4 +1,4 @@ -import React, { useState, useEffect, useCallback, useMemo } from "react" +import React, { useState, useEffect, useMemo, useCallback } from "react" import Box from "@mui/material/Box" import Grid from "@mui/material/Grid2" import Typography from "@mui/material/Typography" @@ -19,28 +19,26 @@ import { GeneAutoComplete2Props, GeneInfo, QueryResponse } from "./types" export const GeneAutocomplete = ( props: GeneAutoComplete2Props ) => { - const { - assembly, - slotProps, - endIcon = 'search', + const { + assembly, + slotProps, + endIcon = 'search', CustomEndIcon, - // onIconClick, - onTextBoxClick, - onGeneSelected, - onGeneSubmitted, - renderOption, - colorTheme - } = props; - - const [inputValue, setInputValue] = useState("") + onGeneSelected, + onGeneSubmitted, + renderOption, + colorTheme + } = props; + const [value, setValue] = useState(props.slotProps?.autocompleteProps?.defaultValue) + const [inputValue, setInputValue] = useState("") const [options, setOptions] = useState([]) const [descriptions, setDescriptions] = useState<{ name: string; desc: string }[]>([]) const [loadingOptions, setLoadingOptions] = useState(false) - //Fetch gene desciptions + //Fetch and set gene desciptions. Descriptions should probably not be it's own state variable, but rather added to options useEffect(() => { const fetchData = async () => { - let descriptions = await Promise.all( + const descriptions = await Promise.all( options.map((gene) => fetch("https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + gene.name.toUpperCase()) .then((x) => x && x.json()) @@ -59,9 +57,10 @@ export const GeneAutocomplete = ( setDescriptions(descriptions) } - options && fetchData() + if (options) fetchData() }, [options]) + //handles setting options on search change const onSearchChange = async (value: string, assembly: string) => { setOptions([]) setLoadingOptions(true) @@ -91,15 +90,14 @@ export const GeneAutocomplete = ( } } }) - setOptions(g) + setOptions(g.sort((a, b) => a.name.localeCompare(b.name))) } else if (genesSuggestion && genesSuggestion.length === 0) { setOptions([]) } setLoadingOptions(false) } - const debounceFn = useMemo(() => debounce(onSearchChange, 500), []) - + const debounceOnSearchChange = useMemo(() => debounce(onSearchChange, 500), []) // Merge the ListboxProps const mergedListboxProps = { @@ -141,38 +139,57 @@ export const GeneAutocomplete = ( ...slotProps?.inputTextFieldProps?.sx } } + + //changes to text input + const handleInputChange = ( + _, + value: string, + ) => { + if (value != "") { debounceOnSearchChange(value, assembly) } //fetch new gene suggestions + setInputValue(value) + } - const attemptSubmit = (inputVal: string) => { - const gene = options.find(x => x.name.toLowerCase() === inputVal.toLowerCase()) - gene && onGeneSubmitted && onGeneSubmitted(gene) - gene && setInputValue(gene.name) - // gene && setValue(gene) + //changes to value of component + const handleChange = ( + _, + value: GeneInfo, + ) => { + setValue(value) + if (onGeneSelected) onGeneSelected(value) } + //checks for enter key and tries to match with listed options + const handleKeyDown = useCallback(( + event: React.KeyboardEvent & { defaultMuiPrevented?: boolean;} + ) => { + if (event.key === "Enter") { + const matchingGene = options.find(x => x.name.toLowerCase() === inputValue.toLowerCase()) + if (matchingGene) { + setValue(matchingGene) + if (onGeneSubmitted) onGeneSubmitted(matchingGene) + } + } + }, [inputValue, onGeneSubmitted, options]) + + const handleIconClick = useCallback(() => { + if (onGeneSubmitted && value) onGeneSubmitted(value) + }, [onGeneSubmitted, value]) + return ( a.name.localeCompare(b.name))} //How do I type this properly? + options={options} + value={value} inputValue={inputValue} - onInputChange={(_, newInputValue) => { - if (newInputValue != "") { - debounceFn(newInputValue, assembly) // This triggers sending new request for genes - } - setInputValue(newInputValue) - }} - onChange={(_, value) => onGeneSelected && onGeneSelected(value)} //Should I just expose the whole onChange function? - onKeyDown={(event) => { - if (event.key === "Enter") { - attemptSubmit(inputValue) - } - }} + onInputChange={handleInputChange} + onChange={handleChange} //Should I just expose the whole onChange function? + onKeyDown={handleKeyDown} noOptionsText={loadingOptions ? "Loading..." : "No Genes Found"} //Maybe expose? renderInput={(params) => ( @@ -206,7 +223,7 @@ export const GeneAutocomplete = ( attemptSubmit(inputValue)} + onClick={handleIconClick} {...mergedIconProps} > {CustomEndIcon ? diff --git a/screen2.0/src/app/search/_geneAutocomplete/types.ts b/screen2.0/src/app/search/_geneAutocomplete/types.ts index bae2cc8a..a461e1e1 100644 --- a/screen2.0/src/app/search/_geneAutocomplete/types.ts +++ b/screen2.0/src/app/search/_geneAutocomplete/types.ts @@ -49,8 +49,6 @@ endIcon?: 'search' | 'add' | 'none' CustomEndIcon?: OverridableComponent> & { muiName: string; } -// onIconClick?: React.MouseEventHandler -onTextBoxClick?: React.MouseEventHandler /** * * Callback fired when a gene is selected from the dropdown options. Not fired on submission (enter, clicking endIcon) diff --git a/screen2.0/src/app/search/mainresultsfilters.tsx b/screen2.0/src/app/search/mainresultsfilters.tsx index 741ec7f2..497ac1eb 100644 --- a/screen2.0/src/app/search/mainresultsfilters.tsx +++ b/screen2.0/src/app/search/mainresultsfilters.tsx @@ -919,9 +919,9 @@ export function MainResultsFilters( null, getOptionDisabled: option => !linkedGenesWithNums.find(x => x.geneName === option.name), }, + inputTextFieldProps: {onClick: () => !dataLinkedGenes && !loadingLinkedGenes && getLinkedGenes()}, stackProps: { mt: 1 } }} - onTextBoxClick={() => !dataLinkedGenes && !loadingLinkedGenes && getLinkedGenes()} endIcon="none" colorTheme="light" onGeneSelected={(gene) => diff --git a/screen2.0/src/app/search/page.tsx b/screen2.0/src/app/search/page.tsx index 84af9abf..e2cd865e 100644 --- a/screen2.0/src/app/search/page.tsx +++ b/screen2.0/src/app/search/page.tsx @@ -20,7 +20,7 @@ import ChevronLeftIcon from '@mui/icons-material/ChevronLeft'; import CloseIcon from '@mui/icons-material/Close'; import Rampage from "./_ccredetails/rampage"; -import { GeneExpression } from "./_ccredetails/geneexpression"; +import { GeneExpression } from "../applets/gene-expression/geneexpression"; import { LoadingMessage } from "../../common/lib/utility" import { Download } from "@mui/icons-material" import { ApolloQueryResult, useLazyQuery } from "@apollo/client" diff --git a/screen2.0/src/graphql/__generated__/gql.ts b/screen2.0/src/graphql/__generated__/gql.ts index d9c287c7..0dd78df5 100644 --- a/screen2.0/src/graphql/__generated__/gql.ts +++ b/screen2.0/src/graphql/__generated__/gql.ts @@ -11,6 +11,7 @@ import { TypedDocumentNode as DocumentNode } from '@graphql-typed-document-node/ * 3. It does not support dead code elimination, so it will add unused operations. * * Therefore it is highly recommended to use the babel or swc plugin for production. + * Learn more about it here: https://the-guild.dev/graphql/codegen/plugins/presets/preset-client#reducing-bundle-size */ const documents = { "\n query RNASeqQuery($assembly: String!){\n rnaSeqQuery(assembly:$assembly) {\n biosample\n }\n }\n": types.RnaSeqQueryDocument, @@ -18,7 +19,7 @@ const documents = { "\nquery cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) {\n cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) {\n accession\n coordinates {\n start\n end\n chromosome\n }\n }\n}\n": types.CCreQueryDocument, "\nquery bedIntersectCCRE_1 ($user_ccres: [cCRE]!, $assembly: String!, $max_ouput_length: Int) {\n intersection (\n userCcres: $user_ccres,\n assembly: $assembly,\n maxOutputLength: $max_ouput_length\n )\n}\n": types.BedIntersectCcre_1Document, "\n query getGeneLocation($name: String!, $assembly: String!) {\n gene(name: [$name], assembly: $assembly, version: 40) {\n coordinates {\n chromosome\n start\n end\n }\n }\n }\n": types.GetGeneLocationDocument, - "\nquery geneexpression($assembly: String!, $accessions: [String], $gene_id: [String]) {\n gene_dataset(accession: $accessions) {\n biosample\n tissue\n \tcell_compartment\n biosample_type\n \tassay_term_name\n accession \n gene_quantification_files(assembly: $assembly) {\n accession\n biorep\n quantifications(gene_id_prefix: $gene_id) {\n tpm\n file_accession\n fpkm\n }\n }\n }\n}\n ": types.GeneexpressionDocument, + "\nquery geneexpression($assembly: String!, $gene_id: [String]) {\n gene_dataset(processed_assembly: $assembly) {\n biosample\n tissue\n \tcell_compartment\n biosample_type\n \tassay_term_name\n accession \n gene_quantification_files(assembly: $assembly) {\n accession\n biorep\n quantifications(gene_id_prefix: $gene_id) {\n tpm\n file_accession\n }\n }\n }\n}\n ": types.GeneexpressionDocument, "\n query geneAutocomplete($assembly: String!, $name: [String!], $limit: Int, $version: Int) {\n gene(assembly: $assembly, name: $name, limit: $limit, version: $version) {\n name\n id\n coordinates {\n start\n chromosome\n end\n }\n }\n } ": types.GeneAutocompleteDocument, "\n query geneOrthologQuery($name: [String]!, $assembly: String!) {\n geneOrthologQuery: geneorthologQuery(name: $name, assembly: $assembly) {\n humanGene: external_gene_name\n mouseGene: mmusculus_homolog_associated_gene_name\n }\n }\n": types.GeneOrthologQueryDocument, "\n query getAllGWASStudies {\n getAllGwasStudies {\n study\n totalldblocks \n author\n pubmedid\n studyname\n \n }\n }\n": types.GetAllGwasStudiesDocument, @@ -98,7 +99,7 @@ export function gql(source: "\n query getGeneLocation($name: String!, $assembly /** * The gql function is used to parse GraphQL queries into a document that can be used by GraphQL clients. */ -export function gql(source: "\nquery geneexpression($assembly: String!, $accessions: [String], $gene_id: [String]) {\n gene_dataset(accession: $accessions) {\n biosample\n tissue\n \tcell_compartment\n biosample_type\n \tassay_term_name\n accession \n gene_quantification_files(assembly: $assembly) {\n accession\n biorep\n quantifications(gene_id_prefix: $gene_id) {\n tpm\n file_accession\n fpkm\n }\n }\n }\n}\n "): (typeof documents)["\nquery geneexpression($assembly: String!, $accessions: [String], $gene_id: [String]) {\n gene_dataset(accession: $accessions) {\n biosample\n tissue\n \tcell_compartment\n biosample_type\n \tassay_term_name\n accession \n gene_quantification_files(assembly: $assembly) {\n accession\n biorep\n quantifications(gene_id_prefix: $gene_id) {\n tpm\n file_accession\n fpkm\n }\n }\n }\n}\n "]; +export function gql(source: "\nquery geneexpression($assembly: String!, $gene_id: [String]) {\n gene_dataset(processed_assembly: $assembly) {\n biosample\n tissue\n \tcell_compartment\n biosample_type\n \tassay_term_name\n accession \n gene_quantification_files(assembly: $assembly) {\n accession\n biorep\n quantifications(gene_id_prefix: $gene_id) {\n tpm\n file_accession\n }\n }\n }\n}\n "): (typeof documents)["\nquery geneexpression($assembly: String!, $gene_id: [String]) {\n gene_dataset(processed_assembly: $assembly) {\n biosample\n tissue\n \tcell_compartment\n biosample_type\n \tassay_term_name\n accession \n gene_quantification_files(assembly: $assembly) {\n accession\n biorep\n quantifications(gene_id_prefix: $gene_id) {\n tpm\n file_accession\n }\n }\n }\n}\n "]; /** * The gql function is used to parse GraphQL queries into a document that can be used by GraphQL clients. */ diff --git a/screen2.0/src/graphql/__generated__/graphql.ts b/screen2.0/src/graphql/__generated__/graphql.ts index 92a9065e..1ccc448b 100644 --- a/screen2.0/src/graphql/__generated__/graphql.ts +++ b/screen2.0/src/graphql/__generated__/graphql.ts @@ -56,70 +56,6 @@ export type Scalars = { federation__Scope: { input: any; output: any; } }; -export type AtacAggregate = { - __typename?: 'ATACAggregate'; - atac_alignments_accession: Scalars['String']['output']; - atac_dataset_accession: Scalars['String']['output']; - forward_values: Array; - motif: Scalars['String']['output']; - peaks_accession: Scalars['String']['output']; - peaks_dataset_accession: Scalars['String']['output']; - reverse_values: Array; -}; - -export type AggregationResult = { - __typename?: 'AggregationResult'; - total: Scalars['Int']['output']; - values: Array>; -}; - -export type AlleleFrequency = { - __typename?: 'AlleleFrequency'; - afr_af?: Maybe; - amr_af?: Maybe; - eas_af?: Maybe; - eur_af?: Maybe; - frequency?: Maybe; - sas_af?: Maybe; - sequence?: Maybe; -}; - -export type Assembly = { - __typename?: 'Assembly'; - /** Returns a collection of datasets that have files processed using this assembly */ - datasets: DatasetCollection; - name: Scalars['String']['output']; - species: Scalars['String']['output']; -}; - -export type BigBedReplicatedPeaks = File & { - __typename?: 'BigBedReplicatedPeaks'; - accession: Scalars['String']['output']; - assembly: Assembly; - dataset: PeakDataset; - type: Scalars['String']['output']; - url?: Maybe; -}; - -export type BigBedUnreplicatedPeaks = File & { - __typename?: 'BigBedUnreplicatedPeaks'; - accession: Scalars['String']['output']; - assembly: Assembly; - biorep?: Maybe; - dataset: PeakDataset; - peaks: Array; - techrep?: Maybe; - type: Scalars['String']['output']; - url?: Maybe; -}; - - -export type BigBedUnreplicatedPeaksPeaksArgs = { - chrom: Scalars['String']['input']; - chrom_end: Scalars['Int']['input']; - chrom_start: Scalars['Int']['input']; -}; - export type BigRequest = { /** Start chromosome */ chr1: Scalars['String']['input']; @@ -142,273 +78,12 @@ export type BigRequest = { zoomLevel?: InputMaybe; }; -export type BigResponse = { - __typename?: 'BigResponse'; - data?: Maybe>>; - error?: Maybe; -}; - -export type BigResponseWithRange = { - __typename?: 'BigResponseWithRange'; - chrom: Scalars['String']['output']; - data?: Maybe; - end: Scalars['Int']['output']; - start: Scalars['Int']['output']; - url: Scalars['String']['output']; -}; - -export type Biosample = { - __typename?: 'Biosample'; - datasets: DatasetCollection; - name: Scalars['String']['output']; - species: Scalars['String']['output']; -}; - -export type BiosamplePartitionCollection = DatasetCollection & { - __typename?: 'BiosamplePartitionCollection'; - biosample: Biosample; - counts: DatasetCounts; - datasets: Array; - partitionByBiosample: Array; - partitionByLab: Array; - partitionByTarget: Array; -}; - - -export type BiosamplePartitionCollectionPartitionByBiosampleArgs = { - name?: InputMaybe; -}; - - -export type BiosamplePartitionCollectionPartitionByLabArgs = { - name?: InputMaybe; -}; - - -export type BiosamplePartitionCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type Caprafccdoubledata = { - __typename?: 'CAPRAFCCDOUBLEDATA'; - dna_rep1: Scalars['Int']['output']; - experiment: Scalars['String']['output']; - fdr: Scalars['Float']['output']; - log2fc: Scalars['Float']['output']; - pvalue: Scalars['Float']['output']; - rdhs_p1: Scalars['String']['output']; - rdhs_p2: Scalars['String']['output']; - rna_rep1: Scalars['Int']['output']; - rna_rep2: Scalars['Int']['output']; - rna_rep3: Scalars['Int']['output']; -}; - -export type Caprafccsolodata = { - __typename?: 'CAPRAFCCSOLODATA'; - dna_rep1: Scalars['Int']['output']; - experiment: Scalars['String']['output']; - fdr: Scalars['Float']['output']; - log2fc: Scalars['Float']['output']; - pvalue: Scalars['Float']['output']; - rdhs: Scalars['String']['output']; - rna_rep1: Scalars['Int']['output']; - rna_rep2: Scalars['Int']['output']; - rna_rep3: Scalars['Int']['output']; -}; - -export type Ccre = GenomicObject & { - __typename?: 'CCRE'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - coordinates: GenomicRange; - group: Scalars['String']['output']; - gtex_decorations: Array; - id: Scalars['String']['output']; - maxZ?: Maybe; - nearby_genes?: Maybe; - rDHS: Scalars['String']['output']; - sequence?: Maybe; - zScores?: Maybe>; -}; - - -export type CcreMaxZArgs = { - assay: Scalars['String']['input']; -}; - - -export type CcreNearby_GenesArgs = { - include_downstream?: InputMaybe; - include_upstream?: InputMaybe; - limit?: InputMaybe; - protein_coding?: InputMaybe; -}; - - -export type CcreSequenceArgs = { - googleProject?: InputMaybe; - twobit_url: Scalars['String']['input']; -}; - - -export type CcrezScoresArgs = { - experiments?: InputMaybe>; -}; - -export type CcreInfo = { - __typename?: 'CCREInfo'; - accession: Scalars['String']['output']; - atacmax: Scalars['Float']['output']; - concordant: Scalars['Boolean']['output']; - ctcfmax: Scalars['Float']['output']; - isproximal: Scalars['Boolean']['output']; - k4me3max: Scalars['Float']['output']; - k27acmax: Scalars['Float']['output']; -}; - -export type CcrezScore = { - __typename?: 'CCREZScore'; - assay: Scalars['String']['output']; - cCRE: Scalars['String']['output']; - experiment_accession: Scalars['String']['output']; - score: Scalars['Float']['output']; -}; - -export type CaQtls = { - __typename?: 'CaQtls'; - snpid?: Maybe; - type?: Maybe; -}; - -export type CalderonAtacData = { - __typename?: 'CalderonAtacData'; - celltype: Scalars['String']['output']; - chromosome: Scalars['String']['output']; - class: Scalars['String']['output']; - donor: Scalars['String']['output']; - end: Scalars['Int']['output']; - group: Scalars['String']['output']; - icre: Scalars['String']['output']; - name: Scalars['String']['output']; - rdhs: Scalars['String']['output']; - start: Scalars['Int']['output']; - stimulation: Scalars['String']['output']; - umap_1: Scalars['Float']['output']; - umap_2: Scalars['Float']['output']; - value: Scalars['Float']['output']; -}; - -export type CalderonCorcesAtacData = { - __typename?: 'CalderonCorcesAtacData'; - celltype: Scalars['String']['output']; - chromosome: Scalars['String']['output']; - class: Scalars['String']['output']; - ct_description: Scalars['String']['output']; - description: Scalars['String']['output']; - donor: Scalars['String']['output']; - end: Scalars['Int']['output']; - group: Scalars['String']['output']; - grouping: Scalars['String']['output']; - icre: Scalars['String']['output']; - name: Scalars['String']['output']; - order: Scalars['Int']['output']; - pmid: Scalars['String']['output']; - rdhs: Scalars['String']['output']; - start: Scalars['Int']['output']; - stimulation: Scalars['String']['output']; - study: Scalars['String']['output']; - subclass: Scalars['String']['output']; - value: Scalars['Float']['output']; -}; - -export type CalderonCorcesByCtAtacData = { - __typename?: 'CalderonCorcesByCtAtacData'; - celltype: Scalars['String']['output']; - chromosome: Scalars['String']['output']; - class: Scalars['String']['output']; - description: Scalars['String']['output']; - end: Scalars['Int']['output']; - group: Scalars['String']['output']; - icre: Scalars['String']['output']; - name: Scalars['String']['output']; - order: Scalars['Int']['output']; - pmid: Scalars['String']['output']; - rdhs: Scalars['String']['output']; - start: Scalars['Int']['output']; - stimulation: Scalars['String']['output']; - study: Scalars['String']['output']; - subclass: Scalars['String']['output']; - value: Scalars['Float']['output']; -}; - -export type CalderonRnaData = { - __typename?: 'CalderonRnaData'; - celltype: Scalars['String']['output']; - class: Scalars['String']['output']; - donor: Scalars['String']['output']; - gene_id: Scalars['String']['output']; - name: Scalars['String']['output']; - stimulation: Scalars['String']['output']; - transcript_ids: Scalars['String']['output']; - umap_1: Scalars['Float']['output']; - umap_2: Scalars['Float']['output']; - value: Scalars['Float']['output']; -}; - -export type CcreLinks = { - __typename?: 'CcreLinks'; - destination: Scalars['String']['output']; - distance: Scalars['Int']['output']; - path: Scalars['String']['output']; - source: Scalars['String']['output']; - weights: Scalars['String']['output']; -}; - -export type CcreLinksDetails = { - __typename?: 'CcreLinksDetails'; - ccrelinks?: Maybe>>; - ccrenodegroups?: Maybe>>; -}; - -export type CcreNodeGroups = { - __typename?: 'CcreNodeGroups'; - accession: Scalars['String']['output']; - ccre_group: Scalars['String']['output']; -}; - -export type CellTypeEnrichment = { - __typename?: 'CellTypeEnrichment'; - encodeid: Scalars['String']['output']; - fdr?: Maybe; - fe?: Maybe; - pValue?: Maybe; -}; - export type CellTypeInput = { celltype: Scalars['String']['input']; celltypedisplayname?: InputMaybe; rnaseq?: InputMaybe; }; -export type Celltype = { - __typename?: 'Celltype'; - celltype?: Maybe; - ct_image_url?: Maybe; - wiki_desc?: Maybe; -}; - -export type CelltypeTf = { - __typename?: 'CelltypeTF'; - celltype: Scalars['String']['output']; - tf: Scalars['String']['output']; -}; - -export type ChromLength = { - __typename?: 'ChromLength'; - chromosome: Scalars['String']['output']; - length: Scalars['Int']['output']; -}; - export type ChromRange = { chromosome: Scalars['String']['input']; start?: InputMaybe; @@ -421,330 +96,11 @@ export type ChromosomeRangeInput = { chrom_start: Scalars['Int']['input']; }; -export type Collection = DatasetCollection & { - __typename?: 'Collection'; - counts: DatasetCounts; - datasets: Array; - partitionByBiosample: Array; - partitionByLab: Array; - partitionByTarget: Array; -}; - - -export type CollectionPartitionByBiosampleArgs = { - name?: InputMaybe; -}; - - -export type CollectionPartitionByLabArgs = { - name?: InputMaybe; -}; - - -export type CollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type ConservationAggregate = { - __typename?: 'ConservationAggregate'; - conservation_type: Scalars['String']['output']; - motif: Scalars['String']['output']; - peaks_accession: Scalars['String']['output']; - peaks_dataset_accession: Scalars['String']['output']; - values: Array; -}; - export type CoordinateInput = { field: Scalars['String']['input']; points: Array; }; -export type Cytoband = { - __typename?: 'Cytoband'; - bandname: Scalars['String']['output']; - coordinates: GenomicRange; - stain: Scalars['String']['output']; -}; - -export type DlMotifPeakOccurrences = { - __typename?: 'DLMotifPeakOccurrences'; - annotation: Scalars['String']['output']; - class_of_transposable_element: Scalars['String']['output']; - consensus_regex?: Maybe; - genomic_region: GenomicRegion; - name: Scalars['String']['output']; - number_of_celltypes_instance_found_in: Scalars['Int']['output']; - number_of_datasets_instance_found_in: Scalars['Int']['output']; - ppm: Array>>; - rdhs: Scalars['String']['output']; - score: Scalars['Float']['output']; - sequence: Scalars['String']['output']; - strand: Scalars['String']['output']; - tf: Scalars['String']['output']; - total_number_of_celltypes_instance_found_in?: Maybe; - total_number_of_datasets_instance_found_in?: Maybe; -}; - -export type DlMotifRdhsOccurrences = { - __typename?: 'DLMotifRdhsOccurrences'; - bound_or_gcr_match: Scalars['String']['output']; - cell_types: Scalars['Float']['output']; - constrained: Scalars['String']['output']; - constrained_score: Scalars['Float']['output']; - datasets: Scalars['Float']['output']; - genomic_context: Scalars['String']['output']; - genomic_region: GenomicRegion; - in_rdhs: Scalars['String']['output']; - instance_id: Scalars['String']['output']; - score: Scalars['Float']['output']; - sequence: Scalars['String']['output']; - strand: Scalars['String']['output']; - tf: Scalars['String']['output']; - z_score: Scalars['Float']['output']; -}; - -export type DNaseAggregate = { - __typename?: 'DNaseAggregate'; - dnase_alignments_accession: Scalars['String']['output']; - dnase_dataset_accession: Scalars['String']['output']; - forward_values: Array; - motif: Scalars['String']['output']; - peaks_accession: Scalars['String']['output']; - peaks_dataset_accession: Scalars['String']['output']; - reverse_values: Array; -}; - -export type DatasetCollection = { - counts: DatasetCounts; - datasets: Array; - partitionByBiosample: Array; - partitionByLab: Array; - partitionByTarget: Array; -}; - - -export type DatasetCollectionPartitionByBiosampleArgs = { - name?: InputMaybe; -}; - - -export type DatasetCollectionPartitionByLabArgs = { - name?: InputMaybe; -}; - - -export type DatasetCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type DatasetCounts = { - __typename?: 'DatasetCounts'; - biosamples: Scalars['Int']['output']; - labs: Scalars['Int']['output']; - projects: Scalars['Int']['output']; - species: Scalars['Int']['output']; - targets: Scalars['Int']['output']; - total: Scalars['Int']['output']; -}; - -export type DeconQtls = { - __typename?: 'DeconQtls'; - adj_beta_pval?: Maybe; - celltype?: Maybe; - geneid?: Maybe; - nom_val?: Maybe; - r_squared?: Maybe; - slope?: Maybe; - snp_chrom?: Maybe; - snp_start?: Maybe; - snpid?: Maybe; -}; - -export type DeepLearnedMotif = { - __typename?: 'DeepLearnedMotif'; - accession: Scalars['String']['output']; - assay?: Maybe; - au_roc?: Maybe; - consensus_regex?: Maybe; - dataset_id: Scalars['String']['output']; - fractional_enrichment?: Maybe; - ppm: Array>>; - protein_type?: Maybe; - roc_curve?: Maybe>>>; - selex_round?: Maybe; - source?: Maybe; - species: Scalars['String']['output']; - tf: Scalars['String']['output']; - total_number_of_celltypes_instance_found_in?: Maybe; - total_number_of_datasets_instance_found_in?: Maybe; -}; - -export type DeepLearnedMotifCount = { - __typename?: 'DeepLearnedMotifCount'; - nonselexdlmotifs: Scalars['Int']['output']; - selexdlmotifs: Scalars['Int']['output']; -}; - -export type DeepLearnedMotitfResponse = { - __typename?: 'DeepLearnedMotitfResponse'; - data?: Maybe; -}; - -export type Deg = { - __typename?: 'Deg'; - base_mean?: Maybe; - celltype?: Maybe; - disease?: Maybe; - gene?: Maybe; - lfc_se?: Maybe; - log2_fc?: Maybe; - padj?: Maybe; - pvalue?: Maybe; - stat?: Maybe; -}; - -export type EbiAssociations = { - __typename?: 'EBIAssociations'; - ccre?: Maybe; - chromosome?: Maybe; - class?: Maybe; - icre?: Maybe; - immu_screen_trait?: Maybe; - link?: Maybe; - mapped_trait?: Maybe; - p_value?: Maybe; - position?: Maybe; - pubmedid?: Maybe; - region?: Maybe; - risk_allele_frequency?: Maybe; - snpid?: Maybe; - strongest_snp_risk_allele?: Maybe; - study?: Maybe; -}; - -export type Eqtl = { - __typename?: 'EQTL'; - celltype?: Maybe; - geneid?: Maybe; - phenotype_id?: Maybe; - pval_beta?: Maybe; - pval_nominal?: Maybe; - pvalue?: Maybe; - qvalue?: Maybe; - rsid?: Maybe; - study: Scalars['String']['output']; - variant_id?: Maybe; -}; - -export type Element = { - __typename?: 'Element'; - category: Scalars['String']['output']; - coordinates: GenomicRange; - name: Scalars['String']['output']; - signal?: Maybe>>; - signal_average?: Maybe; - umap_coordinates: Point; -}; - - -export type ElementCategoryArgs = { - field: Scalars['String']['input']; -}; - - -export type ElementSignalArgs = { - field: Scalars['String']['input']; -}; - - -export type ElementSignal_AverageArgs = { - field: Scalars['String']['input']; -}; - - -export type ElementUmap_CoordinatesArgs = { - field: Scalars['String']['input']; -}; - -export type EnsembleData = { - __typename?: 'EnsembleData'; - biotype?: Maybe; - ccds_id?: Maybe>>; - description?: Maybe; - display_name?: Maybe; - hgnc_primary_id?: Maybe; - hgnc_synonyms?: Maybe>>; - id?: Maybe; - uniprot_primary_id?: Maybe; - uniprot_synonyms?: Maybe>>; - version?: Maybe; -}; - -export type EntexActiveAnnotations = { - __typename?: 'EntexActiveAnnotations'; - assay_score: Scalars['String']['output']; - tissue: Scalars['String']['output']; -}; - -export type EntexData = { - __typename?: 'EntexData'; - accession: Scalars['String']['output']; - assay: Scalars['String']['output']; - donor: Scalars['String']['output']; - experiment_accession: Scalars['String']['output']; - hap1_allele_ratio: Scalars['Float']['output']; - hap1_count: Scalars['Int']['output']; - hap2_count: Scalars['Int']['output']; - imbalance_significance: Scalars['Float']['output']; - p_betabinom: Scalars['Float']['output']; - tissue: Scalars['String']['output']; -}; - -export type Exon = { - __typename?: 'Exon'; - UTRs?: Maybe>>; - coordinates: GenomicRange; - exon_number: Scalars['Int']['output']; - id: Scalars['String']['output']; - name: Scalars['String']['output']; - project: Scalars['String']['output']; - score: Scalars['Int']['output']; - strand: Scalars['String']['output']; -}; - -export type Fcdata = { - __typename?: 'FCDATA'; - assay_result: Scalars['String']['output']; - chromosome: Scalars['String']['output']; - element_id: Scalars['String']['output']; - start: Scalars['Int']['output']; - stop: Scalars['Int']['output']; - tissues: Scalars['String']['output']; -}; - -export type Factor = { - __typename?: 'Factor'; - assembly: Scalars['String']['output']; - color?: Maybe; - coordinates?: Maybe; - dbd?: Maybe>>; - ensemble_data?: Maybe; - factor_wiki?: Maybe; - gene_id?: Maybe; - hgnc_data?: Maybe; - isTF?: Maybe; - modifications?: Maybe; - name: Scalars['String']['output']; - ncbi_data?: Maybe; - pdbids?: Maybe; - uniprot_data?: Maybe; -}; - -export type FieldResult = { - __typename?: 'FieldResult'; - name: Scalars['String']['output']; -}; - export enum FieldType { Category = 'CATEGORY', Coordinates = 'COORDINATES', @@ -752,2464 +108,61 @@ export enum FieldType { SignalMatrix = 'SIGNAL_MATRIX' } -export type File = { - accession: Scalars['String']['output']; - dataset: PeakDataset; - type: Scalars['String']['output']; -}; - -export type FilteredAlignments = File & { - __typename?: 'FilteredAlignments'; - accession: Scalars['String']['output']; - assembly: Assembly; - biorep?: Maybe; - dataset: PeakDataset; - techrep?: Maybe; - type: Scalars['String']['output']; - url?: Maybe; -}; - -export type GtExDecoration = { - __typename?: 'GTExDecoration'; - allele_specific: Scalars['Boolean']['output']; - ctcf_bound: Scalars['Boolean']['output']; - proximal: Scalars['Boolean']['output']; - state: GtExState; - tissue: Scalars['String']['output']; -}; - -export type GtExQtl = { - __typename?: 'GTExQTL'; - chromosome: Scalars['String']['output']; - gene_id: Scalars['String']['output']; - ma_count: Scalars['Int']['output']; - ma_samples: Scalars['Int']['output']; - maf: Scalars['Float']['output']; - min_pval_nominal: Scalars['Float']['output']; - position: Scalars['Int']['output']; - pval_beta: Scalars['Float']['output']; - pval_nominal: Scalars['Float']['output']; - pval_nominal_threshold: Scalars['Float']['output']; - slope: Scalars['Float']['output']; - slope_se: Scalars['Float']['output']; - tissue: Scalars['String']['output']; - tss_distance: Scalars['Int']['output']; -}; - export enum GtExState { Active = 'ACTIVE', Bivalent = 'BIVALENT', Repressed = 'REPRESSED' } -export type Gwas = { - __typename?: 'GWAS'; - author: Scalars['String']['output']; - cellTypeEnrichment?: Maybe>>; - leadSNPs?: Maybe>>; - name: Scalars['String']['output']; - pubMedId: Scalars['Int']['output']; -}; - - -export type GwasCellTypeEnrichmentArgs = { - encodeid?: InputMaybe; - fdr_threshold?: InputMaybe; - fe_threshold?: InputMaybe; - pValue_threshold?: InputMaybe; -}; - - -export type GwasLeadSnPsArgs = { - linkedSNP?: InputMaybe; -}; - -export type GwasCelltypeEnrichment = { - __typename?: 'GWASCelltypeEnrichment'; - accession: Scalars['String']['output']; - celltype: Scalars['String']['output']; - fc: Scalars['Float']['output']; - fdr: Scalars['Float']['output']; - pvalue: Scalars['Float']['output']; -}; - -export type Gene = GenomicObject & { - __typename?: 'Gene'; - assembly: Scalars['String']['output']; - coordinates: GenomicRange; - gene_quantification?: Maybe>>; - gene_type: Scalars['String']['output']; - havana_id?: Maybe; - id: Scalars['String']['output']; - intersecting_ccres?: Maybe; - name: Scalars['String']['output']; - project: Scalars['String']['output']; - score: Scalars['Int']['output']; - strand: Scalars['String']['output']; - transcripts?: Maybe>>; -}; - - -export type GeneGene_QuantificationArgs = { - assembly: Scalars['String']['input']; - experiment_accession?: InputMaybe>>; - file_accession?: InputMaybe>>; - fpkm_range?: InputMaybe; - gene_id?: InputMaybe>>; - limit?: InputMaybe; - offset?: InputMaybe; - sortByTpm?: InputMaybe; - source?: InputMaybe; - tpm_range?: InputMaybe; -}; - - -export type GeneIntersecting_CcresArgs = { - include_downstream?: InputMaybe; - include_upstream?: InputMaybe; -}; - -export type GeneAssociation = { - __typename?: 'GeneAssociation'; - dge_fdr: Scalars['Float']['output']; - dge_log2fc: Scalars['Float']['output']; - disease: Scalars['String']['output']; - gene_id: Scalars['String']['output']; - gene_name: Scalars['String']['output']; - hsq: Scalars['Float']['output']; - twas_bonferroni: Scalars['Float']['output']; - twas_p: Scalars['Float']['output']; -}; - -export type GeneDataset = { - __typename?: 'GeneDataset'; - accession: Scalars['String']['output']; - age_death?: Maybe; - assay_term_name?: Maybe; - biosample: Scalars['String']['output']; - biosample_type?: Maybe; - biosample_value?: Maybe; - cell_compartment?: Maybe; - diagnosis?: Maybe; - fetal?: Maybe; - gene_quantification_files?: Maybe>>; - lab_friendly_name?: Maybe; - lab_name?: Maybe; - metadata?: Maybe; - sex?: Maybe; - signal_files?: Maybe>>; - source: QuantDataSource; - study?: Maybe; - suicidaldeath?: Maybe; - tissue?: Maybe; - transcript_quantification_files?: Maybe>>; - user_collection_accession?: Maybe; -}; - - -export type GeneDatasetGene_Quantification_FilesArgs = { - assembly?: InputMaybe; -}; - - -export type GeneDatasetSignal_FilesArgs = { - assembly?: InputMaybe; -}; - - -export type GeneDatasetTranscript_Quantification_FilesArgs = { - assembly?: InputMaybe; -}; - -export type GeneOrtholog = { - __typename?: 'GeneOrtholog'; - V17?: Maybe; - V18?: Maybe; - chromosome_name?: Maybe; - end_position?: Maybe; - ensembl_gene_id?: Maybe; - external_gene_name?: Maybe; - mmusculus_homolog_associated_gene_name?: Maybe; - mmusculus_homolog_chrom_end?: Maybe; - mmusculus_homolog_chrom_start?: Maybe; - mmusculus_homolog_chromosome?: Maybe; - mmusculus_homolog_ensembl_gene?: Maybe; - mmusculus_homolog_goc_score?: Maybe; - mmusculus_homolog_orthology_type?: Maybe; - mmusculus_homolog_perc_id?: Maybe; - mmusculus_homolog_perc_id_r1?: Maybe; - mmusculus_homolog_wga_coverage?: Maybe; - start_position?: Maybe; - strand?: Maybe; -}; - -export type GeneQuantification = { - __typename?: 'GeneQuantification'; - effective_len: Scalars['Float']['output']; - expected_count: Scalars['Float']['output']; - experiment_accession: Scalars['String']['output']; - file_accession: Scalars['String']['output']; - fpkm: Scalars['Float']['output']; - fpkm_ci_lower_bound: Scalars['Float']['output']; - fpkm_ci_upper_bound: Scalars['Float']['output']; - fpkm_coefficient_of_quartile_variation?: Maybe; - gene?: Maybe; - len: Scalars['Float']['output']; - pme_fpkm: Scalars['Float']['output']; - pme_tpm: Scalars['Float']['output']; - posterior_mean_count: Scalars['Float']['output']; - posterior_standard_deviation_of_count: Scalars['Float']['output']; - tpm: Scalars['Float']['output']; - tpm_ci_lower_bound: Scalars['Float']['output']; - tpm_ci_upper_bound: Scalars['Float']['output']; - tpm_coefficient_of_quartile_variation?: Maybe; -}; - -export type GeneQuantificationFile = { - __typename?: 'GeneQuantificationFile'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - biorep?: Maybe; - dataset_accession: Scalars['String']['output']; - quantifications?: Maybe>>; - techrep?: Maybe; -}; - - -export type GeneQuantificationFileQuantificationsArgs = { - experiment_accession?: InputMaybe>>; - fpkm_range?: InputMaybe; - gene_id?: InputMaybe>>; - gene_id_prefix?: InputMaybe>>; - tpm_range?: InputMaybe; -}; - -export type GenesCountResponse = { - __typename?: 'GenesCountResponse'; - chromosome: Scalars['String']['output']; - count?: Maybe; - end?: Maybe; - start?: Maybe; -}; - -export type GenomeRange = { - __typename?: 'GenomeRange'; - chromosome?: Maybe; - end?: Maybe; - start?: Maybe; -}; - -export type Genomes = { - __typename?: 'Genomes'; - defaultPos?: Maybe; - genome: Scalars['String']['output']; - trackDb: Scalars['String']['output']; -}; - -export type GenomicAssembly = { - __typename?: 'GenomicAssembly'; - description: Scalars['String']['output']; - name: Scalars['String']['output']; - species: Scalars['String']['output']; -}; - -export type GenomicCoordinateRange = GenomicObject & { - __typename?: 'GenomicCoordinateRange'; - assembly: Scalars['String']['output']; - coordinates: GenomicRange; - id: Scalars['String']['output']; -}; - -export type GenomicObject = { - assembly: Scalars['String']['output']; - coordinates: GenomicRange; - id: Scalars['String']['output']; -}; - -/** - * An object with an ID. - * Follows the [Relay Global Object Identification Specification](https://relay.dev/graphql/objectidentification.htm) - */ -export type GenomicRange = { - __typename?: 'GenomicRange'; - chromosome: Scalars['String']['output']; - end: Scalars['Int']['output']; - start: Scalars['Int']['output']; -}; - export type GenomicRangeInput = { chromosome: Scalars['String']['input']; end: Scalars['Int']['input']; start: Scalars['Int']['input']; }; -export type GenomicRegion = { - __typename?: 'GenomicRegion'; - chromosome: Scalars['String']['output']; - end: Scalars['Int']['output']; - start: Scalars['Int']['output']; -}; - export type GenomicRegionInput = { chromosome: Scalars['String']['input']; end: Scalars['Int']['input']; start: Scalars['Int']['input']; }; -export type GtexGenes = { - __typename?: 'GtexGenes'; - description: Scalars['String']['output']; - gene_id: Scalars['String']['output']; - tissue_type: Scalars['String']['output']; - tissue_type_detail: Scalars['String']['output']; - val: Scalars['Float']['output']; -}; - -export type GwasIntersectingSnpsWithBcre = { - __typename?: 'GwasIntersectingSnpsWithBcre'; - associated_gene: Scalars['String']['output']; - association_p_val: Array>; - bcre_group: Scalars['String']['output']; - ccre_chrom: Scalars['String']['output']; - ccre_class: Scalars['String']['output']; - ccre_start: Scalars['Int']['output']; - ccre_stop: Scalars['Int']['output']; - ccreid: Scalars['String']['output']; - disease: Scalars['String']['output']; - rdhsid: Scalars['String']['output']; - riskallele: Scalars['String']['output']; - snp_chrom: Scalars['String']['output']; - snp_start: Scalars['Int']['output']; - snp_stop: Scalars['Int']['output']; - snpid: Scalars['String']['output']; -}; - -export type GwasIntersectingSnpsWithCcre = { - __typename?: 'GwasIntersectingSnpsWithCcre'; - associated_gene: Scalars['String']['output']; - association_p_val: Array>; - ccre_chrom: Scalars['String']['output']; - ccre_class: Scalars['String']['output']; - ccre_start: Scalars['Int']['output']; - ccre_stop: Scalars['Int']['output']; - ccreid: Scalars['String']['output']; - disease: Scalars['String']['output']; - rdhsid: Scalars['String']['output']; - riskallele: Scalars['String']['output']; - snp_chrom: Scalars['String']['output']; - snp_start: Scalars['Int']['output']; - snp_stop: Scalars['Int']['output']; - snpid: Scalars['String']['output']; +export type MotifInstanceInput = { + name: Scalars['String']['input']; + peaks_accession: Scalars['String']['input']; }; -export type GwasMotifEnrichment = { - __typename?: 'GwasMotifEnrichment'; - accession?: Maybe; - background_frequencies: Array; - cell_type?: Maybe; - consensus_regex: Scalars['String']['output']; - e_value: Scalars['Float']['output']; - flank_occurrences_ratio: Scalars['Float']['output']; - flank_p_value: Scalars['Float']['output']; - flank_z_score: Scalars['Float']['output']; - fold_enrichment: Scalars['Float']['output']; - id: Scalars['String']['output']; - lesser_peaks_occurrences_ratio: Scalars['Float']['output']; - name: Scalars['String']['output']; - original_peaks: Scalars['Int']['output']; - original_peaks_occurrences: Scalars['Int']['output']; - p_value: Scalars['Float']['output']; - peak_centrality: Scalars['PeakCentralityData']['output']; - peaks_accession: Scalars['String']['output']; - pwm: Array>>; - shuffled_occurrences_ratio: Scalars['Float']['output']; - shuffled_p_value: Scalars['Float']['output']; - shuffled_z_score: Scalars['Float']['output']; - sites: Scalars['Int']['output']; - study_id: Scalars['Int']['output']; - tomtom_matches?: Maybe>>; +export type PointInput = { + x: Scalars['Float']['input']; + y: Scalars['Float']['input']; }; -export type GwasPeakEnrichment = { - __typename?: 'GwasPeakEnrichment'; - dataset_accession: Scalars['String']['output']; - fdr_d?: Maybe; - fdr_d_m?: Maybe; - fdr_p?: Maybe; - fdr_p_m?: Maybe; - fold_enrichment_d?: Maybe; - fold_enrichment_d_m?: Maybe; - fold_enrichment_p?: Maybe; - fold_enrichment_p_m?: Maybe; - number_of_peaks?: Maybe; - p_value_d?: Maybe; - p_value_d_m?: Maybe; - p_value_p?: Maybe; - p_value_p_m?: Maybe; - pmid: Scalars['String']['output']; - tf: Scalars['String']['output']; -}; +export enum Population { + African = 'AFRICAN', + American = 'AMERICAN', + EastAsian = 'EAST_ASIAN', + European = 'EUROPEAN', + SouthAsian = 'SOUTH_ASIAN' +} -export type GwasSnpAssociation = { - __typename?: 'GwasSnpAssociation'; - analyses_identifying_snp: Scalars['Int']['output']; - associated_gene: Scalars['String']['output']; - association_p_val: Array>; - chrom: Scalars['String']['output']; - disease: Scalars['String']['output']; - riskallele: Scalars['String']['output']; - snpid: Scalars['String']['output']; - start: Scalars['Int']['output']; - stop: Scalars['Int']['output']; +export type PositionInput = { + chromosome: Scalars['String']['input']; + position: Scalars['Int']['input']; }; -export type GwasStudies = { - __typename?: 'GwasStudies'; - author?: Maybe; - pubmedid?: Maybe; - study?: Maybe; - studyname?: Maybe; - totalldblocks?: Maybe; +export type QuantDataSourceInput = { + type?: InputMaybe; + user_collection?: InputMaybe; }; -export type GwasStudySnPs = { - __typename?: 'GwasStudySNPs'; - author: Scalars['String']['output']; - chromosome: Scalars['String']['output']; - ldblock: Scalars['Int']['output']; - ldblocksnpid: Scalars['String']['output']; - pubmedid: Scalars['String']['output']; - rsquare: Scalars['String']['output']; - snpid: Scalars['String']['output']; - start: Scalars['Int']['output']; - stop: Scalars['Int']['output']; - study: Scalars['String']['output']; - studyname: Scalars['String']['output']; -}; - -export type HgncData = { - __typename?: 'HgncData'; - alias_symbol?: Maybe>>; - ccds_id?: Maybe>>; - entrez_id?: Maybe; - gene_group?: Maybe>>; - gene_group_id?: Maybe>>; - hgnc_id?: Maybe; - location?: Maybe; - locus_group?: Maybe; - locus_type?: Maybe; - name?: Maybe; - prev_name?: Maybe>>; - prev_symbol?: Maybe>>; - symbol?: Maybe; - uniprot_ids?: Maybe>>; -}; - -export type HighQualityMemeMotif = { - __typename?: 'HighQualityMemeMotif'; - assembly: Scalars['String']['output']; - background_frequencies: Array; - celltype?: Maybe; - consensus_regex: Scalars['String']['output']; - e_value: Scalars['Float']['output']; - flank_occurrences_ratio: Scalars['Float']['output']; - flank_p_value: Scalars['Float']['output']; - flank_z_score: Scalars['Float']['output']; - lesser_peaks_occurrences_ratio: Scalars['Float']['output']; - original_peaks: Scalars['Int']['output']; - original_peaks_occurrences: Scalars['Int']['output']; - peaks_accession: Scalars['String']['output']; - points?: Maybe; - pwm: Array>>; - shuffled_occurrences_ratio: Scalars['Float']['output']; - shuffled_p_value: Scalars['Float']['output']; - shuffled_z_score: Scalars['Float']['output']; - sites: Scalars['Int']['output']; - target?: Maybe; -}; - -export type HistoneAggregate = { - __typename?: 'HistoneAggregate'; - assembly: Scalars['String']['output']; - distal_values: Array; - histone_dataset_accession: Scalars['String']['output']; - histone_signal_accession: Scalars['String']['output']; - peaks_accession: Scalars['String']['output']; - peaks_dataset_accession: Scalars['String']['output']; - proximal_values: Array; - values: Array; -}; - -export type HistoneAggregatePeakDataset = { - __typename?: 'HistoneAggregatePeakDataset'; - assembly: Scalars['String']['output']; - peaks_accession: Scalars['String']['output']; - peaks_dataset_accession: Scalars['String']['output']; -}; - -export type Icre = { - __typename?: 'ICRE'; - accession: Scalars['String']['output']; - celltypes?: Maybe>>; - coordinates: GenomicRange; - group: Scalars['String']['output']; - rdhs: Scalars['String']['output']; -}; - -export type Icreldr = { - __typename?: 'ICRELDR'; - celltype: Scalars['String']['output']; - coefficient: Scalars['Float']['output']; - coefficient_std_error: Scalars['Float']['output']; - coefficient_zscore: Scalars['Float']['output']; - enrichment: Scalars['Float']['output']; - enrichment_p: Scalars['Float']['output']; - enrichment_std_error: Scalars['Float']['output']; - h2: Scalars['Float']['output']; - h2_std_error: Scalars['Float']['output']; - snps: Scalars['Float']['output']; - study: Scalars['String']['output']; -}; - -export type IntersectingCcrEs = { - __typename?: 'IntersectingCCREs'; - assembly: Scalars['String']['output']; - chromosome?: Maybe; - end?: Maybe; - intersecting_ccres?: Maybe>>; - start?: Maybe; -}; - -export type IntersectingGenes = { - __typename?: 'IntersectingGenes'; - assembly: Scalars['String']['output']; - chromosome?: Maybe; - end?: Maybe; - intersecting_genes?: Maybe>>; - limit?: Maybe; - protein_coding?: Maybe; - start?: Maybe; -}; - -export type LdrEnrichment = { - __typename?: 'LDREnrichment'; - biosample: RegistryBiosample; - conditional_enrichment: Scalars['Float']['output']; - conditional_error: Scalars['Float']['output']; - conditional_p: Scalars['Float']['output']; - enrichment: Scalars['Float']['output']; - enrichment_error: Scalars['Float']['output']; - enrichment_p: Scalars['Float']['output']; - study: Scalars['String']['output']; -}; - -export type Lab = { - __typename?: 'Lab'; - friendly_name?: Maybe; - name?: Maybe; -}; - -export type LabPartitionCollection = DatasetCollection & { - __typename?: 'LabPartitionCollection'; - counts: DatasetCounts; - datasets: Array; - lab: Lab; - partitionByBiosample: Array; - partitionByLab: Array; - partitionByTarget: Array; -}; - - -export type LabPartitionCollectionPartitionByBiosampleArgs = { - name?: InputMaybe; -}; - - -export type LabPartitionCollectionPartitionByLabArgs = { - name?: InputMaybe; -}; - - -export type LabPartitionCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type LinkedGenes = { - __typename?: 'LinkedGenes'; - accession: Scalars['String']['output']; - assay?: Maybe; - assembly: Scalars['String']['output']; - celltype?: Maybe; - displayname?: Maybe; - effectsize?: Maybe; - experiment_accession?: Maybe; - gene: Scalars['String']['output']; - geneid: Scalars['String']['output']; - genetype: Scalars['String']['output']; - grnaid?: Maybe; - method: Scalars['String']['output']; - p_val?: Maybe; - score?: Maybe; - slope?: Maybe; - source?: Maybe; - tissue?: Maybe; - variantid?: Maybe; -}; - -export type LinkedGenesCelltypes = { - __typename?: 'LinkedGenesCelltypes'; - celltype?: Maybe; - displayname?: Maybe; - method?: Maybe; -}; - -export type LinkedSnp = { - __typename?: 'LinkedSNP'; - coordinates?: Maybe; - dPrime: Scalars['Float']['output']; - id: Scalars['String']['output']; - rSquared: Scalars['Float']['output']; - snp?: Maybe; -}; - - -export type LinkedSnpCoordinatesArgs = { - assembly: Scalars['String']['input']; -}; - - -export type LinkedSnpSnpArgs = { - assembly: Scalars['String']['input']; -}; - -export type MafResult = { - __typename?: 'MAFResult'; - minorAlleles: Array; - position: Position; - refAllele: Scalars['String']['output']; - snp: Scalars['String']['output']; -}; - -export type Mprafccdata = { - __typename?: 'MPRAFCCDATA'; - assay_type: Scalars['String']['output']; - barcode_location: Scalars['String']['output']; - celltype: Scalars['String']['output']; - chromosome: Scalars['String']['output']; - element_location: Scalars['String']['output']; - experiment: Scalars['String']['output']; - log2fc: Scalars['Float']['output']; - series: Scalars['String']['output']; - start: Scalars['Int']['output']; - stop: Scalars['Int']['output']; - strand: Scalars['String']['output']; -}; - -export type MemeMotif = { - __typename?: 'MemeMotif'; - background_frequencies: Array; - cell_type: Scalars['String']['output']; - consensus_regex: Scalars['String']['output']; - e_value: Scalars['Float']['output']; - factor: Scalars['String']['output']; - flank_occurrences_ratio: Scalars['Float']['output']; - flank_p_value: Scalars['Float']['output']; - flank_z_score: Scalars['Float']['output']; - id: Scalars['String']['output']; - lesser_peaks_occurrences_ratio: Scalars['Float']['output']; - name: Scalars['String']['output']; - original_peaks: Scalars['Int']['output']; - original_peaks_occurrences: Scalars['Int']['output']; - peak_centrality: Scalars['PeakCentralityData']['output']; - peaks_accession: Scalars['String']['output']; - peaks_file?: Maybe; - pwm: Array>>; - shuffled_occurrences_ratio: Scalars['Float']['output']; - shuffled_p_value: Scalars['Float']['output']; - shuffled_z_score: Scalars['Float']['output']; - sites: Scalars['Int']['output']; - tomtom_matches?: Maybe>; -}; - -export type MemeMotifAlignment = { - __typename?: 'MemeMotifAlignment'; - distance: Scalars['Float']['output']; - motif: MemeMotif; - offset: Scalars['Int']['output']; - reverseComplement: Scalars['Boolean']['output']; -}; - -export type MemeMotifCount = { - __typename?: 'MemeMotifCount'; - count: Scalars['Int']['output']; -}; - -export type MemeMotifOccurrence = { - __typename?: 'MemeMotifOccurrence'; - consensus_regex: Scalars['String']['output']; - genomic_region: GenomicRegion; - motif?: Maybe; - peaks_accession: Scalars['String']['output']; - q_value: Scalars['Float']['output']; - sequence?: Maybe; - strand: Scalars['String']['output']; -}; - - -export type MemeMotifOccurrenceSequenceArgs = { - googleProject?: InputMaybe; - twobit_url: Scalars['String']['input']; -}; - -export type MemeMotifSearchResult = { - __typename?: 'MemeMotifSearchResult'; - results: Array>; - total: Scalars['Int']['output']; -}; - -export type MemeSelexMotif = { - __typename?: 'MemeSelexMotif'; - assay?: Maybe; - name?: Maybe; - peaks_accession?: Maybe; - pwm: Array>>; - selex_round?: Maybe; - study?: Maybe; - target?: Maybe; - tomtom_matches?: Maybe>>; -}; - -export type MethylFileMatch = { - __typename?: 'MethylFileMatch'; - age: Scalars['String']['output']; - age_units: Scalars['String']['output']; - assembly: Scalars['String']['output']; - biosample_ontology_id: Scalars['String']['output']; - donor: Scalars['String']['output']; - life_stage: Scalars['String']['output']; - methyl_bed_accessions: Array; - methyl_dataset_accession: Scalars['String']['output']; - peaks_accession: Scalars['String']['output']; - peaks_dataset_accession: Scalars['String']['output']; -}; - -export type ModificationData = { - __typename?: 'ModificationData'; - amino_acid_code?: Maybe; - modification?: Maybe; - position?: Maybe; -}; - -export type Modifications = { - __typename?: 'Modifications'; - modification?: Maybe>>; - name?: Maybe; - symbol?: Maybe; - title?: Maybe; -}; - -export type MotifAlignment = { - __typename?: 'MotifAlignment'; - distance: Scalars['Float']['output']; - motif: MemeSelexMotif; - offset: Scalars['Int']['output']; - reverseComplement: Scalars['Boolean']['output']; -}; - -export type MotifEnrichment = { - __typename?: 'MotifEnrichment'; - bins: Array; - biosample: Scalars['String']['output']; - motif?: Maybe; - motif_id: Scalars['String']['output']; - p_value: Scalars['Float']['output']; - statistic: Scalars['Float']['output']; - top_enrichment_value: Scalars['Float']['output']; - top_enrichment_z_score: Scalars['Float']['output']; -}; - -export type MotifEnrichmentMatrix = { - __typename?: 'MotifEnrichmentMatrix'; - biosamples: Array; - motif_ids: Array; - z_scores: Array>>; -}; - -export type MotifInstanceInput = { - name: Scalars['String']['input']; - peaks_accession: Scalars['String']['input']; -}; - -export type MotifSearchResult = { - __typename?: 'MotifSearchResult'; - results: Array>; - total: Scalars['Int']['output']; -}; - -export type Mutation = { - __typename?: 'Mutation'; - addcCREs: Array>; - addupdatecCREs: Array>; - create_user_collection: UserCollection; - create_user_dataset: GeneDataset; - create_user_gene_quantification_file: GeneQuantificationFile; - create_user_transcript_quantification_file: GeneQuantificationFile; - delete_user_collection: Scalars['ID']['output']; - delete_user_dataset: Scalars['ID']['output']; - delete_user_gene_quantification_file: Scalars['ID']['output']; - delete_user_transcript_quantification_file: Scalars['ID']['output']; - queue_user_collection_import: Scalars['ID']['output']; - update_user_collection: UserCollection; - update_user_dataset: GeneDataset; - update_user_gene_quantification_file: GeneQuantificationFile; - update_user_transcript_quantification_file: GeneQuantificationFile; -}; - - -export type MutationAddcCrEsArgs = { - accessions?: InputMaybe>>; - uuid: Scalars['String']['input']; -}; - - -export type MutationAddupdatecCrEsArgs = { - accessions?: InputMaybe>>; - uuid: Scalars['String']['input']; -}; - - -export type MutationCreate_User_CollectionArgs = { - is_public?: InputMaybe; - name: Scalars['String']['input']; -}; - - -export type MutationCreate_User_DatasetArgs = { - assay_term_name?: InputMaybe; - biosample: Scalars['String']['input']; - biosample_type?: InputMaybe; - cell_compartment?: InputMaybe; - lab_friendly_name?: InputMaybe; - lab_name?: InputMaybe; - metadata?: InputMaybe; - tissue?: InputMaybe; - user_collection_accession: Scalars['ID']['input']; -}; - - -export type MutationCreate_User_Gene_Quantification_FileArgs = { - assembly?: InputMaybe; - biorep?: InputMaybe; - dataset_accession: Scalars['ID']['input']; - techrep?: InputMaybe; -}; - - -export type MutationCreate_User_Transcript_Quantification_FileArgs = { - assembly?: InputMaybe; - biorep?: InputMaybe; - dataset_accession: Scalars['ID']['input']; - techrep?: InputMaybe; -}; - - -export type MutationDelete_User_CollectionArgs = { - accession: Scalars['ID']['input']; -}; - - -export type MutationDelete_User_DatasetArgs = { - accession: Scalars['ID']['input']; -}; - - -export type MutationDelete_User_Gene_Quantification_FileArgs = { - accession: Scalars['ID']['input']; -}; - - -export type MutationDelete_User_Transcript_Quantification_FileArgs = { - accession: Scalars['ID']['input']; -}; - - -export type MutationQueue_User_Collection_ImportArgs = { - accession: Scalars['ID']['input']; -}; - - -export type MutationUpdate_User_CollectionArgs = { - accession: Scalars['ID']['input']; - is_public?: InputMaybe; - name?: InputMaybe; -}; - - -export type MutationUpdate_User_DatasetArgs = { - accession: Scalars['ID']['input']; - assay_term_name?: InputMaybe; - biosample?: InputMaybe; - biosample_type?: InputMaybe; - cell_compartment?: InputMaybe; - lab_friendly_name?: InputMaybe; - lab_name?: InputMaybe; - metadata?: InputMaybe; - tissue?: InputMaybe; -}; - - -export type MutationUpdate_User_Gene_Quantification_FileArgs = { - accession: Scalars['ID']['input']; - assembly?: InputMaybe; - biorep?: InputMaybe; - techrep?: InputMaybe; -}; - - -export type MutationUpdate_User_Transcript_Quantification_FileArgs = { - accession: Scalars['ID']['input']; - assembly?: InputMaybe; - biorep?: InputMaybe; - techrep?: InputMaybe; -}; - -export type NearbyGenes = { - __typename?: 'NearbyGenes'; - assembly: Scalars['String']['output']; - chromosome?: Maybe; - end: Scalars['Int']['output']; - intersecting_genes: Array; - start: Scalars['Int']['output']; -}; - -export type NearestGenes = { - __typename?: 'NearestGenes'; - distance: Scalars['Int']['output']; - gene: Scalars['String']['output']; -}; - -export type NormalizedSignal = File & { - __typename?: 'NormalizedSignal'; - accession: Scalars['String']['output']; - assembly: Assembly; - biorep?: Maybe; - dataset: PeakDataset; - techrep?: Maybe; - type: Scalars['String']['output']; - url?: Maybe; -}; - -export type Ortholog = { - __typename?: 'Ortholog'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - ortholog: Array>; -}; - -export type PCollection = PeaksCollection & { - __typename?: 'PCollection'; - count?: Maybe; - partitionByTarget: Array; - peaks: Array; -}; - - -export type PCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type Plsgenes = { - __typename?: 'PLSGENES'; - accession: Scalars['String']['output']; - geneid: Scalars['String']['output']; -}; - -export type Peak = { - __typename?: 'Peak'; - chrom: Scalars['String']['output']; - chrom_end: Scalars['Int']['output']; - chrom_start: Scalars['Int']['output']; - dataset: PeakDataset; - experiment_accession: Scalars['String']['output']; - file_accession: Scalars['String']['output']; - name: Scalars['String']['output']; - p_value: Scalars['Float']['output']; - peak: Scalars['Int']['output']; - q_value: Scalars['Float']['output']; - score: Scalars['Int']['output']; - signal_over_peaks?: Maybe; - signal_value: Scalars['Float']['output']; - strand: Scalars['String']['output']; -}; - -export type PeakCount = { - __typename?: 'PeakCount'; - count: Scalars['Int']['output']; -}; - -export type PeakDataset = { - __typename?: 'PeakDataset'; - accession: Scalars['String']['output']; - biosample: Scalars['String']['output']; - cell_slims?: Maybe>>; - developmental_slims?: Maybe>>; - /** - * Returns all files from this dataset. Can filter by the processed assembly. - * NOTE: files with no assembly (i.e. sequence reads) will be returned regardless of assembly filter - * Can also filter by file types. - * Current types are: - * - sequence_reads - * - unfiltered_alignments - * - filtered_alignments - * - unreplicated_peaks - * - replicated_peaks - * - normalized_signal - */ - files: Array; - investigated_as?: Maybe>>; - lab?: Maybe; - organ_slims?: Maybe>>; - project: Scalars['String']['output']; - released?: Maybe; - source: Scalars['String']['output']; - species: Scalars['String']['output']; - system_slims?: Maybe>>; - target?: Maybe; -}; - - -export type PeakDatasetFilesArgs = { - assembly?: InputMaybe; - types?: InputMaybe>; -}; - -export type PeaksCollection = { - count?: Maybe; - partitionByTarget: Array; - peaks: Array; -}; - - -export type PeaksCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type PeaksCounts = { - __typename?: 'PeaksCounts'; - peaks: Scalars['Int']['output']; - total: Scalars['Int']['output']; -}; - -export type PeaksFile = { - __typename?: 'PeaksFile'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - biosample: Scalars['String']['output']; - dataset?: Maybe; - dataset_accession: Scalars['String']['output']; - target: Scalars['String']['output']; -}; - -export type PeaksResponse = { - __typename?: 'PeaksResponse'; - data?: Maybe; - error?: Maybe; -}; - -export type Point = { - __typename?: 'Point'; - x: Scalars['Float']['output']; - y: Scalars['Float']['output']; -}; - -export type PointInput = { - x: Scalars['Float']['input']; - y: Scalars['Float']['input']; -}; - -export type Points = { - __typename?: 'Points'; - x: Scalars['Float']['output']; - y: Scalars['Float']['output']; -}; - -export enum Population { - African = 'AFRICAN', - American = 'AMERICAN', - EastAsian = 'EAST_ASIAN', - European = 'EUROPEAN', - SouthAsian = 'SOUTH_ASIAN' -} - -export type Position = { - __typename?: 'Position'; - chromosome: Scalars['String']['output']; - position: Scalars['Int']['output']; -}; - -export type PositionInput = { - chromosome: Scalars['String']['input']; - position: Scalars['Int']['input']; -}; - -export type PsychEncodeDatasetValues = { - __typename?: 'PsychEncodeDatasetValues'; - avgexp?: Maybe; - celltype?: Maybe; - dataset?: Maybe; - gene?: Maybe; - pctexp?: Maybe; -}; - -export type QtlSigAssoc = { - __typename?: 'QtlSigAssoc'; - dist?: Maybe; - fdr?: Maybe; - geneid?: Maybe; - npval?: Maybe; - qtltype?: Maybe; - slope?: Maybe; - snpid?: Maybe; -}; - -export type QuantDataSource = { - __typename?: 'QuantDataSource'; - type?: Maybe; - user_collection?: Maybe; -}; - -export type QuantDataSourceInput = { - type?: InputMaybe; - user_collection?: InputMaybe; -}; - -export enum QuantDataSourceType { - Encode = 'ENCODE', - PsychEncode = 'PSYCH_ENCODE', - User = 'USER' -} - -export type QuantificationRange = { - high: Scalars['Float']['input']; - low: Scalars['Float']['input']; -}; - -export type Query = { - __typename?: 'Query'; - aggregationQuery: AggregationResult; - assemblies: Array; - atac_aggregate?: Maybe>; - /** Request BigWig / BigBed data */ - bigRequests: Array; - biosamples: Array; - cCREQuery: Array; - cCRESCREENSearch: Array; - cQTLQuery: Array; - calderonAtacUmapQuery?: Maybe>>; - calderonRnaUmapQuery?: Maybe>>; - calderoncorcesAtacQuery?: Maybe>>; - calderoncorcesByCtAtacQuery?: Maybe>>; - capraFccDoubleQuery?: Maybe>>; - capraFccSoloQuery?: Maybe>>; - caqtls?: Maybe>>; - ccREBiosampleQuery: RegistryBiosampleCollection; - celltype?: Maybe>>; - chromlengths?: Maybe>>; - conservation_aggregate?: Maybe>; - createTrackhubQuery: Scalars['String']['output']; - createicresFilesQuery: Scalars['String']['output']; - cytoband?: Maybe>>; - deconqtlsQuery?: Maybe>>; - deep_learned_motif_peak_occurrences?: Maybe>>; - deep_learned_motif_rdhs_occurrences?: Maybe>>; - deep_learned_motifs?: Maybe>>; - deep_learned_motifs_counts?: Maybe; - deep_learned_motifs_data?: Maybe; - degQuery?: Maybe>>; - dnase_aggregate?: Maybe>; - eQTLQuery: Array; - ebiAssociationsQuery?: Maybe>>; - elementQuery: Array>; - entexActiveAnnotationsQuery?: Maybe>>; - entexQuery?: Maybe>>; - factor?: Maybe>>; - fieldQuery: Array>; - functionalCharacterizationQuery?: Maybe>>; - gene?: Maybe>>; - gene_count?: Maybe>>; - gene_dataset?: Maybe>>; - gene_quantification?: Maybe>>; - geneorthologQuery?: Maybe>>; - genesAssociationsQuery?: Maybe>>; - genomeWideAssociationQuery: Array; - genomicAssemblies?: Maybe>>; - getAllGwasStudies?: Maybe>>; - getGWASCtEnrichmentQuery?: Maybe>>; - getLinkedGenesCelltypes?: Maybe>>; - getPedatasetValuesbyCelltypeQuery?: Maybe>>; - getPedatasetValuesbySubclassQuery?: Maybe>>; - getSNPsforGWASStudies?: Maybe>>; - getcCRELinksQuery?: Maybe; - getcCRENodeCelltypes?: Maybe>>; - getcCRETFQuery?: Maybe>>; - getcartAccessionsQuery?: Maybe>; - gettssRampagePeaks?: Maybe>>; - groundLevelVersionsQuery: Array; - gtexQTLQuery: Array; - gtex_genes?: Maybe>>; - gwas_motif_enrichment?: Maybe>>; - gwas_peak_enrichment?: Maybe>>; - gwasintersectingSnpsWithBcreQuery?: Maybe>>; - gwasintersectingSnpsWithCcreQuery?: Maybe>>; - gwassnpAssociationsQuery?: Maybe>>; - highquality_meme_motifs?: Maybe>>; - histone_aggregate_peak_datasets?: Maybe>; - histone_aggregate_values?: Maybe>; - iCRELdrQuery?: Maybe>>; - iCRELdrStudiesQuery: Array; - iCREQuery: Array; - iCREsCountQuery?: Maybe; - icreeQTLQuery?: Maybe>>; - intersection?: Maybe>>; - ldr: Array; - linkedGenesQuery: Array>; - maf: Array; - meme_methyl_motifs?: Maybe>>; - meme_methyl_occurrences?: Maybe>>; - meme_motif_count?: Maybe; - meme_motif_search?: Maybe>>; - meme_motif_search_query?: Maybe>>; - meme_motifs?: Maybe>>; - meme_occurrences?: Maybe>>; - methyl_file_matches?: Maybe>>; - motif_enrichment?: Maybe>; - motif_enrichment_biosamples?: Maybe>; - motif_enrichment_matrix?: Maybe; - mpraFccQuery?: Maybe>>; - my_user_collections: Array>; - nearby_genes?: Maybe>>; - nearestGenes: Array; - orthologQuery?: Maybe>>; - peakCount?: Maybe; - peakDataset: DatasetCollection; - peaks: PeaksCollection; - peaks_files?: Maybe>>; - peaksrange?: Maybe; - peaksrangecount?: Maybe; - plsGenesQuery?: Maybe>>; - public_user_collections: Array>; - qtlsigassocQuery?: Maybe>>; - rDHSQuery: Array; - rampageQuery?: Maybe>>; - rdhs_motif_occurrences?: Maybe>>; - rdhs_motif_occurrences_count?: Maybe; - refseqgenes?: Maybe>>; - refseqxenogenes?: Maybe>>; - resolve: Array; - rnaSeqQuery?: Maybe>>; - singleCellBoxPlotQuery?: Maybe>>; - singleCellGenesQuery?: Maybe>>; - singleCellUmapQuery?: Maybe>>; - snpAssociationsQuery?: Maybe>>; - snpAutocompleteQuery: Array; - snpDensityQuery: Array; - snpQuery: Array; - species: Array; - specific_elements?: Maybe>>; - suggest: Array; - target_motifs?: Maybe>>; - targets: Array; - /** Request Trackhub data */ - trackHubRequests: TrackHubResponse; - transcript?: Maybe>>; - transcript_quantification?: Maybe>>; - tssrampageQuery?: Maybe>>; - user_collection?: Maybe; - vistaQuery: Array; - zScoreQuery: Array; -}; - - -export type QueryAggregationQueryArgs = { - coordinates?: InputMaybe>; - dataset: Scalars['String']['input']; - field: Scalars['String']['input']; - ids?: InputMaybe>>; - umap_polygon?: InputMaybe; -}; - - -export type QueryAssembliesArgs = { - assembly?: InputMaybe; - searchterm?: InputMaybe>>; - species?: InputMaybe; -}; - - -export type QueryAtac_AggregateArgs = { - assembly?: InputMaybe; - atac_alignments_accession?: InputMaybe; - atac_dataset_accession?: InputMaybe; - limit?: InputMaybe; - motif?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe>; - peaks_dataset_accession?: InputMaybe; -}; - - -export type QueryBigRequestsArgs = { - googleProject?: InputMaybe; - requests: Array; -}; - - -export type QueryBiosamplesArgs = { - biosample_prefix?: InputMaybe; - exclude_investigatedas?: InputMaybe>>; - include_investigatedas?: InputMaybe>>; - lab?: InputMaybe; - limit?: InputMaybe; - processed_assembly?: InputMaybe; - project?: InputMaybe; - replicated_peaks?: InputMaybe; - searchterm?: InputMaybe>>; - species?: InputMaybe; - target?: InputMaybe; -}; - - -export type QueryCCreQueryArgs = { - accession?: InputMaybe>; - accession_prefix?: InputMaybe>; - activeInAnyBiosample?: InputMaybe>; - activeInBiosamples?: InputMaybe>; - assembly: Scalars['String']['input']; - coordinates?: InputMaybe>; - group?: InputMaybe>; - limit?: InputMaybe; - rDHS?: InputMaybe>; -}; - - -export type QueryCCrescreenSearchArgs = { - accessions?: InputMaybe>; - assembly: Scalars['String']['input']; - cellType?: InputMaybe; - coordinates?: InputMaybe>>; - element_type?: InputMaybe; - gene_all_end?: InputMaybe; - gene_all_start?: InputMaybe; - gene_pc_end?: InputMaybe; - gene_pc_start?: InputMaybe; - limit?: InputMaybe; - mammals_max?: InputMaybe; - mammals_min?: InputMaybe; - nearbygenesdistancethreshold?: InputMaybe; - nearbygeneslimit?: InputMaybe; - primates_max?: InputMaybe; - primates_min?: InputMaybe; - rank_atac_end?: InputMaybe; - rank_atac_start?: InputMaybe; - rank_ctcf_end?: InputMaybe; - rank_ctcf_start?: InputMaybe; - rank_dnase_end?: InputMaybe; - rank_dnase_start?: InputMaybe; - rank_enhancer_end?: InputMaybe; - rank_enhancer_start?: InputMaybe; - rank_promoter_end?: InputMaybe; - rank_promoter_start?: InputMaybe; - uuid?: InputMaybe; - vertebrates_max?: InputMaybe; - vertebrates_min?: InputMaybe; -}; - - -export type QueryCQtlQueryArgs = { - assembly: Scalars['String']['input']; - coordinates?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - peakId?: InputMaybe; - snpId?: InputMaybe; - strand?: InputMaybe; -}; - - -export type QueryCalderonAtacUmapQueryArgs = { - accession: Scalars['String']['input']; -}; - - -export type QueryCalderonRnaUmapQueryArgs = { - gene_id: Scalars['String']['input']; -}; - - -export type QueryCalderoncorcesAtacQueryArgs = { - accession?: InputMaybe>>; - celltype?: InputMaybe>>; - study?: InputMaybe>>; -}; - - -export type QueryCalderoncorcesByCtAtacQueryArgs = { - accession?: InputMaybe>>; - celltype?: InputMaybe>>; - study?: InputMaybe>>; -}; - - -export type QueryCapraFccDoubleQueryArgs = { - accession: Array>; -}; - - -export type QueryCapraFccSoloQueryArgs = { - accession: Array>; -}; - - -export type QueryCaqtlsArgs = { - snpid: Scalars['String']['input']; -}; - - -export type QueryCcReBiosampleQueryArgs = { - assay?: InputMaybe>; - assembly: Scalars['String']['input']; - name?: InputMaybe>; - umap_coordinates?: InputMaybe>; -}; - - -export type QueryCelltypeArgs = { - assembly: Scalars['String']['input']; - name?: InputMaybe>>; -}; - - -export type QueryChromlengthsArgs = { - assembly: Scalars['String']['input']; - chromosome?: InputMaybe; - limit?: InputMaybe; - maxLength?: InputMaybe; - minLength?: InputMaybe; - offset?: InputMaybe; -}; - - -export type QueryConservation_AggregateArgs = { - assembly?: InputMaybe; - conservation_type?: InputMaybe; - limit?: InputMaybe; - motif?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe>; - peaks_dataset_accession?: InputMaybe; -}; - - -export type QueryCreateTrackhubQueryArgs = { - assembly: Scalars['String']['input']; - celltypes: Array>; - uuid: Scalars['String']['input']; -}; - - -export type QueryCreateicresFilesQueryArgs = { - accession?: InputMaybe>; - accession_prefix?: InputMaybe>; - allcelltypes?: InputMaybe>>>>; - celltypes?: InputMaybe>>>>; - coordinates?: InputMaybe>; - excludecelltypes?: InputMaybe>>>>; - group?: InputMaybe>; - limit?: InputMaybe; - rDHS?: InputMaybe>; - uuid: Scalars['String']['input']; -}; - - -export type QueryCytobandArgs = { - assembly: Scalars['String']['input']; - bandname?: InputMaybe>>; - chromosome?: InputMaybe; - coordinates?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - stain?: InputMaybe>>; -}; - - -export type QueryDeconqtlsQueryArgs = { - geneid?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QueryDeep_Learned_Motif_Peak_OccurrencesArgs = { - genomic_region: Array; - tf?: InputMaybe; -}; - - -export type QueryDeep_Learned_Motif_Rdhs_OccurrencesArgs = { - constrained_score_threshold?: InputMaybe; - genomic_region: Array; - rdhs?: InputMaybe; - sequence?: InputMaybe; - tf?: InputMaybe; - z_score_threshold?: InputMaybe; -}; - - -export type QueryDeep_Learned_MotifsArgs = { - accession?: InputMaybe; - assay?: InputMaybe; - protein_type?: InputMaybe; - selex_round?: InputMaybe>>; - source?: InputMaybe; - species?: InputMaybe; - tf?: InputMaybe; -}; - - -export type QueryDeep_Learned_Motifs_CountsArgs = { - accession?: InputMaybe; - assay?: InputMaybe; - protein_type?: InputMaybe; - selex_round?: InputMaybe>>; - source?: InputMaybe; - species?: InputMaybe; - tf?: InputMaybe; -}; - - -export type QueryDeep_Learned_Motifs_DataArgs = { - accession?: InputMaybe; - assay?: InputMaybe; - protein_type?: InputMaybe; - selex_round?: InputMaybe>>; - source?: InputMaybe; - species?: InputMaybe; - tf?: InputMaybe; -}; - - -export type QueryDegQueryArgs = { - celltype?: InputMaybe; - disease: Scalars['String']['input']; - gene?: InputMaybe; -}; - - -export type QueryDnase_AggregateArgs = { - assembly?: InputMaybe; - dnase_alignments_accession?: InputMaybe; - dnase_dataset_accession?: InputMaybe; - limit?: InputMaybe; - motif?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe>; - peaks_dataset_accession?: InputMaybe; -}; - - -export type QueryEQtlQueryArgs = { - assembly: Scalars['String']['input']; - coordinates?: InputMaybe; - geneId?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - snpId?: InputMaybe; - strand?: InputMaybe; -}; - - -export type QueryEbiAssociationsQueryArgs = { - accession?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QueryElementQueryArgs = { - coordinates?: InputMaybe>; - dataset: Scalars['String']['input']; - ids?: InputMaybe>>; - umap_polygon?: InputMaybe; -}; - - -export type QueryEntexActiveAnnotationsQueryArgs = { - coordinates: GenomicRangeInput; -}; - - -export type QueryEntexQueryArgs = { - accession: Scalars['String']['input']; -}; - - -export type QueryFactorArgs = { - assembly: Scalars['String']['input']; - id?: InputMaybe>>; - isTF?: InputMaybe; - limit?: InputMaybe; - name?: InputMaybe>>; - name_prefix?: InputMaybe; -}; - - -export type QueryFieldQueryArgs = { - dataset: Scalars['String']['input']; - type: FieldType; -}; - - -export type QueryFunctionalCharacterizationQueryArgs = { - assembly: Scalars['String']['input']; - coordinates?: InputMaybe>; -}; - - -export type QueryGeneArgs = { - assembly: Scalars['String']['input']; - chromosome?: InputMaybe; - end?: InputMaybe; - gene_type?: InputMaybe; - havana_id?: InputMaybe; - id?: InputMaybe>>; - limit?: InputMaybe; - name?: InputMaybe>>; - name_prefix?: InputMaybe>; - offset?: InputMaybe; - orderby?: InputMaybe; - start?: InputMaybe; - strand?: InputMaybe; - version?: InputMaybe; -}; - - -export type QueryGene_CountArgs = { - assembly: Scalars['String']['input']; - gene_type?: InputMaybe; - havana_id?: InputMaybe; - id?: InputMaybe>>; - name?: InputMaybe>>; - name_prefix?: InputMaybe>; - range?: InputMaybe>>; - strand?: InputMaybe; -}; - - -export type QueryGene_DatasetArgs = { - accession?: InputMaybe>>; - assay_term_name?: InputMaybe>>; - biosample?: InputMaybe>>; - biosample_type?: InputMaybe>>; - biosample_value?: InputMaybe>>; - cell_compartment?: InputMaybe>>; - diagnosis?: InputMaybe>>; - lab?: InputMaybe>>; - life_stage?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - sex?: InputMaybe>>; - source?: InputMaybe; - study?: InputMaybe>>; - suicidaldeath?: InputMaybe; - tissue?: InputMaybe>>; - user_collection_accession?: InputMaybe>>; -}; - - -export type QueryGene_QuantificationArgs = { - assembly: Scalars['String']['input']; - experiment_accession?: InputMaybe>>; - file_accession?: InputMaybe>>; - fpkm_range?: InputMaybe; - gene_id?: InputMaybe>>; - gene_id_prefix?: InputMaybe>>; - limit?: InputMaybe; - offset?: InputMaybe; - sortByTpm?: InputMaybe; - source?: InputMaybe; - tpm_range?: InputMaybe; -}; - - -export type QueryGeneorthologQueryArgs = { - assembly: Scalars['String']['input']; - name: Array>; -}; - - -export type QueryGenesAssociationsQueryArgs = { - disease: Scalars['String']['input']; - gene_id?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; -}; - - -export type QueryGenomeWideAssociationQueryArgs = { - assembly: Scalars['String']['input']; - pmIds?: InputMaybe>>; -}; - - -export type QueryGenomicAssembliesArgs = { - description?: InputMaybe; - name?: InputMaybe; - searchTerm?: InputMaybe; - species?: InputMaybe; -}; - - -export type QueryGetGwasCtEnrichmentQueryArgs = { - study: Scalars['String']['input']; -}; - - -export type QueryGetPedatasetValuesbyCelltypeQueryArgs = { - dataset: Array>; - gene: Scalars['String']['input']; -}; - - -export type QueryGetPedatasetValuesbySubclassQueryArgs = { - dataset: Array>; - gene: Scalars['String']['input']; -}; - - -export type QueryGetSnPsforGwasStudiesArgs = { - study: Array; -}; - - -export type QueryGetcCreLinksQueryArgs = { - accession: Scalars['String']['input']; - celltype: Scalars['String']['input']; - degree_of_separation: Scalars['Int']['input']; - method?: InputMaybe; -}; - - -export type QueryGetcCreNodeCelltypesArgs = { - accession: Scalars['String']['input']; - method?: InputMaybe; -}; - - -export type QueryGetcCretfQueryArgs = { - accession: Scalars['String']['input']; - assembly: Scalars['String']['input']; -}; - - -export type QueryGetcartAccessionsQueryArgs = { - uuid: Scalars['String']['input']; -}; - - -export type QueryGettssRampagePeaksArgs = { - coordinates: ChromRange; -}; - - -export type QueryGtexQtlQueryArgs = { - assembly: Scalars['String']['input']; - coordinates?: InputMaybe; - gene_id?: InputMaybe>; - ma_count?: InputMaybe; - ma_samples?: InputMaybe; - maf_max?: InputMaybe; - maf_min?: InputMaybe; - pval_beta?: InputMaybe; - tissue?: InputMaybe>; -}; - - -export type QueryGtex_GenesArgs = { - gene_id: Array>; - tissue?: InputMaybe>>; - tissue_subcategory?: InputMaybe>>; -}; - - -export type QueryGwas_Motif_EnrichmentArgs = { - accession?: InputMaybe; - cell_type?: InputMaybe; - name?: InputMaybe; - study_id?: InputMaybe; -}; - - -export type QueryGwas_Peak_EnrichmentArgs = { - number_of_peaks_threshold?: InputMaybe; - pmid: Scalars['String']['input']; -}; - - -export type QueryGwasintersectingSnpsWithBcreQueryArgs = { - bcre_group?: InputMaybe; - disease: Scalars['String']['input']; - limit?: InputMaybe; - offset?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QueryGwasintersectingSnpsWithCcreQueryArgs = { - disease: Scalars['String']['input']; - limit?: InputMaybe; - offset?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QueryGwassnpAssociationsQueryArgs = { - disease: Scalars['String']['input']; - limit?: InputMaybe; - offset?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QueryHighquality_Meme_MotifsArgs = { - assembly: Scalars['String']['input']; - celltype?: InputMaybe; - peaks_accessions?: InputMaybe>>; - target?: InputMaybe; -}; - - -export type QueryHistone_Aggregate_Peak_DatasetsArgs = { - assembly?: InputMaybe; - peaks_accession?: InputMaybe>>; - peaks_dataset_accession?: InputMaybe; -}; - - -export type QueryHistone_Aggregate_ValuesArgs = { - assembly?: InputMaybe; - bin_size?: InputMaybe; - histone_dataset_accession?: InputMaybe; - histone_signal_accession?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe>>; - peaks_dataset_accession?: InputMaybe; - xrange?: InputMaybe; -}; - - -export type QueryICreLdrQueryArgs = { - celltype?: InputMaybe>>; - study?: InputMaybe>>; -}; - - -export type QueryICreQueryArgs = { - accession?: InputMaybe>; - accession_prefix?: InputMaybe>; - allcelltypes?: InputMaybe>>>>; - celltypes?: InputMaybe>>>>; - coordinates?: InputMaybe>; - excludecelltypes?: InputMaybe>>>>; - group?: InputMaybe>; - limit?: InputMaybe; - rDHS?: InputMaybe>; -}; - - -export type QueryICrEsCountQueryArgs = { - accession?: InputMaybe>; - accession_prefix?: InputMaybe>; - allcelltypes?: InputMaybe>>>>; - celltypes?: InputMaybe>>>>; - coordinates?: InputMaybe>; - excludecelltypes?: InputMaybe>>>>; - group?: InputMaybe>; - limit?: InputMaybe; - rDHS?: InputMaybe>; -}; - - -export type QueryIcreeQtlQueryArgs = { - geneid?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - phenotype_id?: InputMaybe; - rsid?: InputMaybe; - study: Scalars['String']['input']; -}; - - -export type QueryIntersectionArgs = { - assembly: Scalars['String']['input']; - maxOutputLength?: InputMaybe; - userCcres: Array>; -}; - - -export type QueryLdrArgs = { - experiment?: InputMaybe>; - study?: InputMaybe>; -}; - - -export type QueryLinkedGenesQueryArgs = { - accession: Array>; - assembly: Scalars['String']['input']; - celltype?: InputMaybe>>; - method?: InputMaybe>>; -}; - - -export type QueryMafArgs = { - positions: Array; -}; - - -export type QueryMeme_Methyl_MotifsArgs = { - consensus_regex?: InputMaybe; - consensus_search?: InputMaybe; - e_value_threshold?: InputMaybe; - flank_p_value_threshold?: InputMaybe; - flank_z_score_threshold?: InputMaybe; - lesser_peaks_occurrences_ratio_threshold?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe>>; - shuffled_p_value_threshold?: InputMaybe; - shuffled_z_score_threshold?: InputMaybe; -}; - - -export type QueryMeme_Methyl_OccurrencesArgs = { - consensus_regex?: InputMaybe; - genomic_region?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe; -}; - - -export type QueryMeme_Motif_CountArgs = { - assembly?: InputMaybe; - consensus_regex?: InputMaybe; - consensus_search?: InputMaybe; - e_value_threshold?: InputMaybe; - flank_p_value_threshold?: InputMaybe; - flank_z_score_threshold?: InputMaybe; - lesser_peaks_occurrences_ratio_threshold?: InputMaybe; - peaks_accession?: InputMaybe>>; - shuffled_p_value_threshold?: InputMaybe; - shuffled_z_score_threshold?: InputMaybe; -}; - - -export type QueryMeme_Motif_SearchArgs = { - assembly: Scalars['String']['input']; - limit?: InputMaybe; - offset?: InputMaybe; - pwms: Array>>>>; -}; - - -export type QueryMeme_Motif_Search_QueryArgs = { - assembly: Scalars['String']['input']; - limit?: InputMaybe; - offset?: InputMaybe; - pwms: Array>>>>; -}; - - -export type QueryMeme_MotifsArgs = { - cell_type?: InputMaybe>; - consensus_regex?: InputMaybe; - consensus_search?: InputMaybe; - e_value_threshold?: InputMaybe; - factor?: InputMaybe>; - flank_p_value_threshold?: InputMaybe; - flank_z_score_threshold?: InputMaybe; - id?: InputMaybe>>; - lesser_peaks_occurrences_ratio_threshold?: InputMaybe; - limit?: InputMaybe; - name?: InputMaybe>>; - offset?: InputMaybe; - peaks_accession?: InputMaybe>>; - shuffled_p_value_threshold?: InputMaybe; - shuffled_z_score_threshold?: InputMaybe; -}; - - -export type QueryMeme_OccurrencesArgs = { - consensus_regex?: InputMaybe; - genomic_region?: InputMaybe>; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe; -}; - - -export type QueryMethyl_File_MatchesArgs = { - assembly?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe; - peaks_dataset_accession?: InputMaybe; -}; - - -export type QueryMotif_EnrichmentArgs = { - biosample?: InputMaybe; - dataset: Scalars['String']['input']; - motif_id?: InputMaybe; -}; - - -export type QueryMotif_Enrichment_BiosamplesArgs = { - dataset: Scalars['String']['input']; -}; - - -export type QueryMotif_Enrichment_MatrixArgs = { - dataset: Scalars['String']['input']; -}; - - -export type QueryMpraFccQueryArgs = { - coordinates?: InputMaybe>; -}; - - -export type QueryNearby_GenesArgs = { - assembly: Scalars['String']['input']; - chromosome: Scalars['String']['input']; - distanceThreshold?: InputMaybe; - end: Scalars['Int']['input']; - gene_type?: InputMaybe>>; - limit?: InputMaybe; - offset?: InputMaybe; - start: Scalars['Int']['input']; -}; - - -export type QueryNearestGenesArgs = { - assembly: Scalars['String']['input']; - coordinates: ChromRange; - limit?: InputMaybe; - protein_coding?: InputMaybe; -}; - - -export type QueryOrthologQueryArgs = { - accession?: InputMaybe>>; - assembly?: InputMaybe; -}; - - -export type QueryPeakCountArgs = { - assay?: InputMaybe; - assembly?: InputMaybe; -}; - - -export type QueryPeakDatasetArgs = { - accession?: InputMaybe>>; - biosample?: InputMaybe; - cell_slims?: InputMaybe>>; - developmental_slims?: InputMaybe>>; - exclude_investigatedas?: InputMaybe>>; - include_investigatedas?: InputMaybe>>; - lab?: InputMaybe; - organ_slims?: InputMaybe>>; - processed_assembly?: InputMaybe; - project?: InputMaybe; - replicated_peak_accession?: InputMaybe; - replicated_peaks?: InputMaybe; - searchterm?: InputMaybe>>; - source?: InputMaybe; - species?: InputMaybe; - system_slims?: InputMaybe>>; - target?: InputMaybe; -}; - - -export type QueryPeaksArgs = { - assembly?: InputMaybe; - experiment_accession?: InputMaybe; - file_accession?: InputMaybe; - range: Array>; - searchterm?: InputMaybe>>; - target?: InputMaybe; - type?: InputMaybe>>; -}; - - -export type QueryPeaks_FilesArgs = { - accession?: InputMaybe; - assembly?: InputMaybe; - dataset_accession?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; -}; - - -export type QueryPeaksrangeArgs = { - assembly?: InputMaybe; - biosample?: InputMaybe; - experiment_accession?: InputMaybe; - file_accession?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - orderby?: InputMaybe; - range: Array>; - target?: InputMaybe; - type?: InputMaybe>>; -}; - - -export type QueryPeaksrangecountArgs = { - assembly?: InputMaybe; - biosample?: InputMaybe; - experiment_accession?: InputMaybe; - file_accession?: InputMaybe; - limit?: InputMaybe; - range: Array>; - target?: InputMaybe; - type?: InputMaybe>>; -}; - - -export type QueryPlsGenesQueryArgs = { - accession?: InputMaybe>>; - geneid?: InputMaybe>>; - geneid_prefix?: InputMaybe>>; -}; - - -export type QueryPublic_User_CollectionsArgs = { - limit?: InputMaybe; - offset?: InputMaybe; -}; - - -export type QueryQtlsigassocQueryArgs = { - geneid?: InputMaybe; - qtltype?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QueryRDhsQueryArgs = { - accession?: InputMaybe>; - activeInAnyBiosample?: InputMaybe>; - activeInBiosamples?: InputMaybe>; - assembly: Scalars['String']['input']; - coordinates?: InputMaybe>; -}; - - -export type QueryRampageQueryArgs = { - transcript_ids?: InputMaybe>; -}; - - -export type QueryRdhs_Motif_OccurrencesArgs = { - assembly?: InputMaybe; - consensus_regex?: InputMaybe; - genomic_region?: InputMaybe>; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe; - rdhss?: InputMaybe>>; -}; - - -export type QueryRdhs_Motif_Occurrences_CountArgs = { - assembly?: InputMaybe; - consensus_regex?: InputMaybe; - genomic_region?: InputMaybe>; - limit?: InputMaybe; - offset?: InputMaybe; - peaks_accession?: InputMaybe; - rdhss?: InputMaybe>>; -}; - - -export type QueryRefseqgenesArgs = { - assembly: Scalars['String']['input']; - chromosome?: InputMaybe; - coordinates?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - searchTerm?: InputMaybe; -}; - - -export type QueryRefseqxenogenesArgs = { - assembly: Scalars['String']['input']; - chromosome?: InputMaybe; - coordinates?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - searchTerm?: InputMaybe; -}; - - -export type QueryResolveArgs = { - assembly: Scalars['String']['input']; - id: Scalars['String']['input']; - limit?: InputMaybe; -}; - - -export type QueryRnaSeqQueryArgs = { - assembly: Scalars['String']['input']; - biosample?: InputMaybe>>; -}; - - -export type QuerySingleCellBoxPlotQueryArgs = { - celltype?: InputMaybe>>; - disease: Scalars['String']['input']; - gene?: InputMaybe>>; - limit?: InputMaybe; - offset?: InputMaybe; -}; - - -export type QuerySingleCellGenesQueryArgs = { - barcodekey?: InputMaybe>>; - disease: Scalars['String']['input']; - featureid?: InputMaybe>>; - featurekey?: InputMaybe>>; -}; - - -export type QuerySingleCellUmapQueryArgs = { - disease: Scalars['String']['input']; -}; - - -export type QuerySnpAssociationsQueryArgs = { - disease: Scalars['String']['input']; - limit?: InputMaybe; - offset?: InputMaybe; - snpid?: InputMaybe; -}; - - -export type QuerySnpAutocompleteQueryArgs = { - assembly: Scalars['String']['input']; - common?: InputMaybe; - limit?: InputMaybe; - offset?: InputMaybe; - snpid: Scalars['String']['input']; -}; - - -export type QuerySnpDensityQueryArgs = { - assembly: Scalars['String']['input']; - coordinates?: InputMaybe>>; - resolution: Scalars['Int']['input']; -}; - - -export type QuerySnpQueryArgs = { - af_threshold?: InputMaybe; - assembly: Scalars['String']['input']; - common?: InputMaybe; - coordinates?: InputMaybe>>; - snpids?: InputMaybe>>; -}; - - -export type QuerySpeciesArgs = { - biosample?: InputMaybe; - lab?: InputMaybe; - project?: InputMaybe; - searchterm?: InputMaybe>>; - target?: InputMaybe; -}; - - -export type QuerySpecific_ElementsArgs = { - dataset: Scalars['String']['input']; - rank_end?: InputMaybe; - rank_start?: InputMaybe; - rdhss?: InputMaybe>; - tissue?: InputMaybe; -}; - - -export type QuerySuggestArgs = { - assembly: Scalars['String']['input']; - id: Scalars['String']['input']; - limit?: InputMaybe; -}; - - -export type QueryTarget_MotifsArgs = { - e_value_threshold?: InputMaybe; - limit?: InputMaybe; - motif_id?: InputMaybe>>; - offset?: InputMaybe; - p_value_threshold?: InputMaybe; - peaks_accessions?: InputMaybe>>; - q_value_threshold?: InputMaybe; - query_motifs?: InputMaybe>; - target_id?: InputMaybe>>; -}; - - -export type QueryTargetsArgs = { - exclude_investigatedas?: InputMaybe>>; - include_investigatedas?: InputMaybe>>; - lab?: InputMaybe; - limit?: InputMaybe; - processed_assembly?: InputMaybe; - project?: InputMaybe; - replicated_peaks?: InputMaybe; - searchterm?: InputMaybe>>; - species?: InputMaybe; - target?: InputMaybe; - target_prefix?: InputMaybe; -}; - - -export type QueryTrackHubRequestsArgs = { - googleProject?: InputMaybe; - trackhuburl: TrackHubUrl; -}; - - -export type QueryTranscriptArgs = { - assembly: Scalars['String']['input']; - chromosome?: InputMaybe; - end?: InputMaybe; - id?: InputMaybe>>; - limit?: InputMaybe; - name?: InputMaybe>>; - name_prefix?: InputMaybe>; - offset?: InputMaybe; - orderby?: InputMaybe; - start?: InputMaybe; - strand?: InputMaybe; - version?: InputMaybe; -}; - - -export type QueryTranscript_QuantificationArgs = { - assembly: Scalars['String']['input']; - experiment_accession?: InputMaybe>>; - file_accession?: InputMaybe>>; - fpkm_range?: InputMaybe; - gene_id?: InputMaybe>>; - limit?: InputMaybe; - offset?: InputMaybe; - sortByTpm?: InputMaybe; - source?: InputMaybe; - tpm_range?: InputMaybe; - transcript_id?: InputMaybe>>; -}; - - -export type QueryTssrampageQueryArgs = { - genename?: InputMaybe; - peakId?: InputMaybe; -}; - - -export type QueryUser_CollectionArgs = { - accession: Scalars['ID']['input']; -}; - - -export type QueryVistaQueryArgs = { - accession?: InputMaybe>; - active?: InputMaybe; - assembly: Scalars['String']['input']; - cCRE?: InputMaybe>; - coordinates?: InputMaybe; - minimumOverlap?: InputMaybe; - tissues?: InputMaybe>; -}; - - -export type QueryZScoreQueryArgs = { - assembly: Scalars['String']['input']; - experiment?: InputMaybe>; - maximum_score?: InputMaybe; - minimum_score?: InputMaybe; - rDHS?: InputMaybe>; -}; - -export type Rdhs = GenomicObject & { - __typename?: 'RDHS'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - coordinates: GenomicRange; - id: Scalars['String']['output']; - maxZ?: Maybe; - sequence: Scalars['String']['output']; - zScores?: Maybe>; -}; - - -export type RdhsMaxZArgs = { - assay: Scalars['String']['input']; -}; - - -export type RdhsSequenceArgs = { - half_width?: InputMaybe; -}; - - -export type RdhszScoresArgs = { - experiments?: InputMaybe>; -}; - -export type RdhsMotifOccurrence = { - __typename?: 'RDHSMotifOccurrence'; - consensus_regex: Scalars['String']['output']; - genomic_region: GenomicRegion; - motif?: Maybe; - p_value: Scalars['Float']['output']; - peaks_accession: Scalars['String']['output']; - rdhs: Scalars['String']['output']; - start_offset: Scalars['Int']['output']; - strand: Scalars['String']['output']; -}; - -export type RdhsMotifOccurrenceCount = { - __typename?: 'RDHSMotifOccurrenceCount'; - count: Scalars['Int']['output']; -}; +export enum QuantDataSourceType { + Encode = 'ENCODE', + PsychEncode = 'PSYCH_ENCODE', + User = 'USER' +} -export type RampageResponse = { - __typename?: 'RampageResponse'; - biosampleType?: Maybe; - chrom?: Maybe; - end?: Maybe; - expAccession?: Maybe; - fileAccession?: Maybe; - geneId?: Maybe; - lifeStage?: Maybe; - name?: Maybe; - organ?: Maybe; - start?: Maybe; - strand?: Maybe; - tissue?: Maybe; - transcriptId?: Maybe; - type?: Maybe; - value?: Maybe; +export type QuantificationRange = { + high: Scalars['Float']['input']; + low: Scalars['Float']['input']; }; export type Range = { @@ -3217,320 +170,6 @@ export type Range = { start?: InputMaybe; }; -export type RefSeqExon = { - __typename?: 'RefSeqExon'; - UTRs?: Maybe>>; - coordinates: GenomicRange; - exon_number: Scalars['Int']['output']; - id: Scalars['String']['output']; - name: Scalars['String']['output']; - project: Scalars['String']['output']; - score: Scalars['Int']['output']; - strand: Scalars['String']['output']; -}; - -export type RefSeqGene = { - __typename?: 'RefSeqGene'; - id: Scalars['String']['output']; - strand: Scalars['String']['output']; - transcripts: Array>; -}; - -export type RefSeqTranscript = { - __typename?: 'RefSeqTranscript'; - coordinates: GenomicRange; - exons?: Maybe>>; - id: Scalars['String']['output']; - name: Scalars['String']['output']; - project: Scalars['String']['output']; - score: Scalars['Int']['output']; - strand: Scalars['String']['output']; -}; - -export type RefSeqUtr = { - __typename?: 'RefSeqUTR'; - coordinates: GenomicRange; - strand: Scalars['String']['output']; -}; - -export type RegistryBiosample = { - __typename?: 'RegistryBiosample'; - cCREZScores: Array; - displayname: Scalars['String']['output']; - experimentAccession?: Maybe; - fileAccession?: Maybe; - ldr_enrichment?: Maybe>; - lifeStage: Scalars['String']['output']; - name: Scalars['String']['output']; - ontology: Scalars['String']['output']; - sampleType: Scalars['String']['output']; - umap_coordinates?: Maybe>; - zscore_histogram: Array; -}; - - -export type RegistryBiosampleCCrezScoresArgs = { - accession?: InputMaybe>; - coordinates?: InputMaybe>; - ctcf_bound?: InputMaybe; - group?: InputMaybe>; - rDHS?: InputMaybe>; -}; - - -export type RegistryBiosampleExperimentAccessionArgs = { - assay: Scalars['String']['input']; -}; - - -export type RegistryBiosampleFileAccessionArgs = { - assay: Scalars['String']['input']; -}; - - -export type RegistryBiosampleLdr_EnrichmentArgs = { - studies?: InputMaybe>; -}; - - -export type RegistryBiosampleUmap_CoordinatesArgs = { - assay: Scalars['String']['input']; -}; - - -export type RegistryBiosampleZscore_HistogramArgs = { - assay: Scalars['String']['input']; - assembly: Scalars['String']['input']; - histogram_bins: Scalars['Int']['input']; - histogram_maximum: Scalars['Int']['input']; - histogram_minimum: Scalars['Int']['input']; -}; - -export type RegistryBiosampleCollection = { - __typename?: 'RegistryBiosampleCollection'; - biosamples?: Maybe>; - specificElements?: Maybe>; -}; - - -export type RegistryBiosampleCollectionSpecificElementsArgs = { - assay: Scalars['String']['input']; -}; - -export type ReplicatedPeaks = File & { - __typename?: 'ReplicatedPeaks'; - accession: Scalars['String']['output']; - assembly: Assembly; - dataset: PeakDataset; - type: Scalars['String']['output']; - url?: Maybe; -}; - -export type RequestError = { - __typename?: 'RequestError'; - errortype?: Maybe; - message?: Maybe; -}; - -export type RnaSeqData = { - __typename?: 'RnaSeqData'; - biosample: Scalars['String']['output']; - expid: Scalars['String']['output']; - negfileid?: Maybe; - posfileid?: Maybe; - unstrandedfileid?: Maybe; -}; - -export type ScreenCellTypeSpecificResponse = { - __typename?: 'SCREENCellTypeSpecificResponse'; - atac_zscore?: Maybe; - ct?: Maybe; - ctcf_zscore?: Maybe; - dnase_zscore?: Maybe; - h3k4me3_zscore?: Maybe; - h3k27ac_zscore?: Maybe; -}; - -export type ScreenNearbyGenes = { - __typename?: 'SCREENNearbyGenes'; - accession: Scalars['String']['output']; - all: IntersectingGenes; - pc: IntersectingGenes; -}; - -export type ScreenSearchResult = { - __typename?: 'SCREENSearchResult'; - atac_zscore: Scalars['Float']['output']; - chrom: Scalars['String']['output']; - ctcf_zscore: Scalars['Float']['output']; - ctspecific?: Maybe; - dnase_zscore: Scalars['Float']['output']; - enhancer_zscore: Scalars['Float']['output']; - in_cart: Scalars['Int']['output']; - info: CcreInfo; - len: Scalars['Int']['output']; - mammals?: Maybe; - maxz: Scalars['Float']['output']; - nearestgenes: Array>; - pct: Scalars['String']['output']; - primates?: Maybe; - promoter_zscore: Scalars['Float']['output']; - rfacets: Array; - sct: Scalars['Float']['output']; - start: Scalars['Int']['output']; - vertebrates?: Maybe; - vistaids?: Maybe>; -}; - -export type Snp = GenomicObject & { - __typename?: 'SNP'; - assembly: Scalars['String']['output']; - autocompleteSimilarity?: Maybe; - coordinates: GenomicRange; - genomeWideAssociation?: Maybe>>; - gtex_eQTLs: Array; - id: Scalars['String']['output']; - intersecting_ccres?: Maybe; - linkageDisequilibrium?: Maybe>>; - minorAlleleFrequency?: Maybe>>; - refAllele?: Maybe; - refFrequency?: Maybe; -}; - - -export type SnpGtex_EQtLsArgs = { - gene_id?: InputMaybe>; - pval_beta?: InputMaybe; - tissue?: InputMaybe>; -}; - - -export type SnpLinkageDisequilibriumArgs = { - dPrimeThreshold?: InputMaybe; - population: Population; - rSquaredThreshold?: InputMaybe; - subpopulation?: InputMaybe; -}; - -export type SnpDensity = { - __typename?: 'SNPDensity'; - common: Scalars['Int']['output']; - coordinates: GenomicRange; - total: Scalars['Int']['output']; -}; - -export type ScoredElement = { - __typename?: 'ScoredElement'; - element: Rdhs; - specificity: Scalars['Float']['output']; -}; - -export type SequenceReads = File & { - __typename?: 'SequenceReads'; - accession: Scalars['String']['output']; - biorep?: Maybe; - dataset: PeakDataset; - paired_end: Scalars['Boolean']['output']; - read_id: Scalars['Int']['output']; - techrep?: Maybe; - type: Scalars['String']['output']; - url?: Maybe; -}; - -export type SignalFile = { - __typename?: 'SignalFile'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - biorep?: Maybe; - dataset_accession: Scalars['String']['output']; - strand?: Maybe; - techrep?: Maybe; - unique_reads?: Maybe; -}; - -export type SinglCellBoxPlot = { - __typename?: 'SinglCellBoxPlot'; - celltype: Scalars['String']['output']; - disease: Scalars['String']['output']; - expr_frac: Scalars['Float']['output']; - firstquartile: Scalars['Float']['output']; - gene: Scalars['String']['output']; - max: Scalars['Float']['output']; - mean_count: Scalars['Float']['output']; - median: Scalars['Float']['output']; - min: Scalars['Float']['output']; - thirdquartile: Scalars['Float']['output']; -}; - -export type SingleBigResponse = { - __typename?: 'SingleBigResponse'; - data?: Maybe; - error?: Maybe; -}; - -export type SingleCellGene = { - __typename?: 'SingleCellGene'; - anno?: Maybe; - azimuth?: Maybe; - barcodekey?: Maybe; - celltype?: Maybe; - channel?: Maybe; - featureid?: Maybe; - featurekey?: Maybe; - individualid?: Maybe; - n_cells?: Maybe; - n_counts?: Maybe; - n_genes?: Maybe; - percent_cells?: Maybe; - sampleid?: Maybe; - subclass?: Maybe; - umap_1?: Maybe; - umap_2?: Maybe; - val?: Maybe; -}; - -export type SingleCellType = { - __typename?: 'SingleCellType'; - anno?: Maybe; - azimuth?: Maybe; - barcodekey?: Maybe; - celltype?: Maybe; - channel?: Maybe; - individualid?: Maybe; - n_counts?: Maybe; - n_genes?: Maybe; - sampleid?: Maybe; - subclass?: Maybe; - umap_1?: Maybe; - umap_2?: Maybe; -}; - -export type SnpAssociation = { - __typename?: 'SnpAssociation'; - a1: Scalars['String']['output']; - a2: Scalars['String']['output']; - chisq?: Maybe; - disease: Scalars['String']['output']; - n: Scalars['Float']['output']; - snpid: Scalars['String']['output']; - z: Scalars['Float']['output']; -}; - -export type Species = { - __typename?: 'Species'; - datasets: DatasetCollection; - name: Scalars['String']['output']; -}; - -export type SpecificElement = { - __typename?: 'SpecificElement'; - location: GenomicRegion; - rank: Scalars['Int']['output']; - rdhs: Scalars['String']['output']; - tissue: Scalars['String']['output']; - value?: Maybe; -}; - export enum SubPopulation { AfricanAmerican = 'AFRICAN_AMERICAN', AfricanCaribbean = 'AFRICAN_CARIBBEAN', @@ -3560,253 +199,6 @@ export enum SubPopulation { Yoruba = 'YORUBA' } -export type Target = { - __typename?: 'Target'; - datasets: DatasetCollection; - name?: Maybe; - target_desc?: Maybe; -}; - -export type TargetMotif = { - __typename?: 'TargetMotif'; - e_value: Scalars['Float']['output']; - jaspar_name?: Maybe; - motifid: Scalars['String']['output']; - optimal_offset: Scalars['Int']['output']; - orientation: Scalars['String']['output']; - overlap: Scalars['Int']['output']; - p_value: Scalars['Float']['output']; - peaks_accession: Scalars['String']['output']; - q_value: Scalars['Float']['output']; - query_id: Scalars['String']['output']; - sites: Scalars['Int']['output']; - target_id: Scalars['String']['output']; -}; - -export type TargetPartitionCollection = DatasetCollection & { - __typename?: 'TargetPartitionCollection'; - counts: DatasetCounts; - datasets: Array; - partitionByBiosample: Array; - partitionByLab: Array; - partitionByTarget: Array; - /** Null only if all datasets in this collection do not have a target. */ - target?: Maybe; -}; - - -export type TargetPartitionCollectionPartitionByBiosampleArgs = { - name?: InputMaybe; -}; - - -export type TargetPartitionCollectionPartitionByLabArgs = { - name?: InputMaybe; -}; - - -export type TargetPartitionCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type TargetPeaks = { - __typename?: 'TargetPeaks'; - name?: Maybe; - peaks: PeaksCollection; -}; - -export type TargetPeaksPartitionCollection = PeaksCollection & { - __typename?: 'TargetPeaksPartitionCollection'; - count?: Maybe; - partitionByTarget: Array; - peaks: Array; - /** Null only if all datasets in this collection do not have a target. */ - target?: Maybe; -}; - - -export type TargetPeaksPartitionCollectionPartitionByTargetArgs = { - name?: InputMaybe; -}; - -export type TrackHub = TrackHubResponse & { - __typename?: 'TrackHub'; - trackHubContent: Scalars['String']['output']; - trackhubname?: Maybe; -}; - -export type TrackHubGenomes = TrackHubResponse & { - __typename?: 'TrackHubGenomes'; - genomes: Array>; - trackhubname?: Maybe; -}; - -export type Transcript = GenomicObject & { - __typename?: 'Transcript'; - assembly: Scalars['String']['output']; - associated_ccres_pls?: Maybe; - coordinates: GenomicRange; - exons?: Maybe>>; - havana_id?: Maybe; - id: Scalars['String']['output']; - intersecting_ccres?: Maybe; - name: Scalars['String']['output']; - project: Scalars['String']['output']; - score: Scalars['Int']['output']; - strand: Scalars['String']['output']; - support_level?: Maybe; - tag?: Maybe; - transcript_type: Scalars['String']['output']; -}; - - -export type TranscriptIntersecting_CcresArgs = { - include_downstream?: InputMaybe; - include_upstream?: InputMaybe; -}; - -export type TranscriptQuantification = { - __typename?: 'TranscriptQuantification'; - effective_len: Scalars['Float']['output']; - expected_count: Scalars['Float']['output']; - experiment_accession: Scalars['String']['output']; - file_accession: Scalars['String']['output']; - fpkm: Scalars['Float']['output']; - fpkm_ci_lower_bound: Scalars['Float']['output']; - fpkm_ci_upper_bound: Scalars['Float']['output']; - fpkm_coefficient_of_quartile_variation?: Maybe; - gene?: Maybe; - iso_pct: Scalars['Float']['output']; - iso_pct_from_pme_tpm: Scalars['Float']['output']; - len: Scalars['Int']['output']; - pme_fpkm: Scalars['Float']['output']; - pme_tpm: Scalars['Float']['output']; - posterior_mean_count: Scalars['Float']['output']; - posterior_standard_deviation_of_count: Scalars['Float']['output']; - tpm: Scalars['Float']['output']; - tpm_ci_lower_bound: Scalars['Float']['output']; - tpm_ci_upper_bound: Scalars['Float']['output']; - tpm_coefficient_of_quartile_variation?: Maybe; - transcript?: Maybe; -}; - -export type TranscriptQuantificationFile = { - __typename?: 'TranscriptQuantificationFile'; - accession: Scalars['String']['output']; - assembly: Scalars['String']['output']; - biorep?: Maybe; - dataset_accession: Scalars['String']['output']; - quantifications?: Maybe>>; - techrep?: Maybe; -}; - - -export type TranscriptQuantificationFileQuantificationsArgs = { - experiment_accession?: InputMaybe>>; - fpkm_range?: InputMaybe; - gene_id?: InputMaybe>>; - gene_id_prefix?: InputMaybe>>; - tpm_range?: InputMaybe; - transcript_id?: InputMaybe>>; - transcript_id_prefix?: InputMaybe>>; -}; - -export type TssPeaksGenes = { - __typename?: 'TssPeaksGenes'; - geneName?: Maybe; - locusType?: Maybe; -}; - -export type TssPeaksResponse = { - __typename?: 'TssPeaksResponse'; - chrom?: Maybe; - end?: Maybe; - genes?: Maybe>>; - peakId?: Maybe; - peakType?: Maybe; - start?: Maybe; -}; - -export type TssRampageResponse = { - __typename?: 'TssRampageResponse'; - biosampleName?: Maybe; - biosampleSummary?: Maybe; - biosampleType?: Maybe; - chrom?: Maybe; - end?: Maybe; - end1?: Maybe; - expAccession?: Maybe; - genes?: Maybe>>; - organ?: Maybe; - peakId?: Maybe; - peakType?: Maybe; - start?: Maybe; - start1?: Maybe; - strand?: Maybe; - value?: Maybe; -}; - -export type TwoBitData = { - __typename?: 'TwoBitData'; - chrom: Scalars['String']['output']; - data?: Maybe>>>>; - end: Scalars['Int']['output']; - start: Scalars['Int']['output']; - url: Scalars['String']['output']; -}; - -export type Utr = { - __typename?: 'UTR'; - coordinates: GenomicRange; - direction: Scalars['Int']['output']; - id: Scalars['String']['output']; - name: Scalars['String']['output']; - parent_protein: Scalars['String']['output']; - phase: Scalars['Int']['output']; - project: Scalars['String']['output']; - score: Scalars['Int']['output']; - strand: Scalars['String']['output']; - tag: Scalars['String']['output']; -}; - -export type UnfilteredAlignments = File & { - __typename?: 'UnfilteredAlignments'; - accession: Scalars['String']['output']; - assembly: Assembly; - biorep?: Maybe; - dataset: PeakDataset; - techrep?: Maybe; - type: Scalars['String']['output']; - url?: Maybe; -}; - -export type UnreplicatedPeaks = File & { - __typename?: 'UnreplicatedPeaks'; - accession: Scalars['String']['output']; - assembly: Assembly; - biorep?: Maybe; - dataset: PeakDataset; - peaks: Array; - techrep?: Maybe; - type: Scalars['String']['output']; - url?: Maybe; -}; - - -export type UnreplicatedPeaksPeaksArgs = { - chrom: Scalars['String']['input']; - chrom_end: Scalars['Int']['input']; - chrom_start: Scalars['Int']['input']; -}; - -export type UserCollection = { - __typename?: 'UserCollection'; - accession: Scalars['ID']['output']; - import_status?: Maybe; - is_public: Scalars['Boolean']['output']; - name: Scalars['String']['output']; -}; - export enum UserCollectionImportStatus { Error = 'ERROR', InProgress = 'IN_PROGRESS', @@ -3814,78 +206,6 @@ export enum UserCollectionImportStatus { Success = 'SUCCESS' } -export type VistaEnhancer = { - __typename?: 'VistaEnhancer'; - accession: Scalars['String']['output']; - active: Scalars['Boolean']['output']; - cCRE: Scalars['String']['output']; - coordinates: GenomicRange; - overlap: Scalars['Int']['output']; - tissues: Array; -}; - -export type ZScore = { - __typename?: 'ZScore'; - experiment: Scalars['String']['output']; - rDHS: Scalars['String']['output']; - score: Scalars['Float']['output']; -}; - -export type ZScoreHistogramBin = { - __typename?: 'ZScoreHistogramBin'; - bin: Scalars['Float']['output']; - count: Scalars['Int']['output']; -}; - -export type CQtl = { - __typename?: 'cQTL'; - coordinates: GenomicRange; - distance: Scalars['Int']['output']; - fdr: Scalars['Float']['output']; - is_top_snp: Scalars['Int']['output']; - n_tested_snps: Scalars['Int']['output']; - peak_coordinates: GenomicRange; - peak_id: Scalars['String']['output']; - pval: Scalars['Float']['output']; - regression_slope: Scalars['Float']['output']; - snp: Scalars['String']['output']; - strand: Scalars['String']['output']; -}; - -export type EQtl = { - __typename?: 'eQTL'; - coordinates: GenomicRange; - distance_to_tss: Scalars['Int']['output']; - fdr: Scalars['Float']['output']; - gene_id: Scalars['String']['output']; - is_top_snp: Scalars['Int']['output']; - n_tested_snps: Scalars['Int']['output']; - pval: Scalars['Float']['output']; - regression_slope: Scalars['Float']['output']; - snp: Scalars['String']['output']; - strand: Scalars['String']['output']; -}; - -export type GroundLevelVersionsEntries = { - __typename?: 'groundLevelVersionsEntries'; - accession: Scalars['String']['output']; - assay: Scalars['String']['output']; - biosample: Scalars['String']['output']; - version: Scalars['String']['output']; -}; - -export type OrthologcCre = { - __typename?: 'orthologcCRE'; - accession: Scalars['String']['output']; - chromosome?: Maybe; - start?: Maybe; - stop?: Maybe; -}; - -export type TrackHubResponse = { - trackhubname?: Maybe; -}; - export type TrackHubUrl = { hubUrl: Scalars['Boolean']['input']; trackHubUrl?: InputMaybe; @@ -3934,12 +254,11 @@ export type GetGeneLocationQuery = { __typename?: 'Query', gene?: Array<{ __type export type GeneexpressionQueryVariables = Exact<{ assembly: Scalars['String']['input']; - accessions?: InputMaybe> | InputMaybe>; gene_id?: InputMaybe> | InputMaybe>; }>; -export type GeneexpressionQuery = { __typename?: 'Query', gene_dataset?: Array<{ __typename?: 'GeneDataset', biosample: string, tissue?: string | null, cell_compartment?: string | null, biosample_type?: string | null, assay_term_name?: string | null, accession: string, gene_quantification_files?: Array<{ __typename?: 'GeneQuantificationFile', accession: string, biorep?: number | null, quantifications?: Array<{ __typename?: 'GeneQuantification', tpm: number, file_accession: string, fpkm: number } | null> | null } | null> | null } | null> | null }; +export type GeneexpressionQuery = { __typename?: 'Query', gene_dataset?: Array<{ __typename?: 'GeneDataset', biosample: string, tissue?: string | null, cell_compartment?: string | null, biosample_type?: string | null, assay_term_name?: string | null, accession: string, gene_quantification_files?: Array<{ __typename?: 'GeneQuantificationFile', accession: string, biorep?: number | null, quantifications?: Array<{ __typename?: 'GeneQuantification', tpm: number, file_accession: string } | null> | null } | null> | null } | null> | null }; export type GeneAutocompleteQueryVariables = Exact<{ assembly: Scalars['String']['input']; @@ -4310,7 +629,7 @@ export const Biosamples_1Document = {"kind":"Document","definitions":[{"kind":"O export const CCreQueryDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"cCREQuery"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"accession_prefix"}},"type":{"kind":"ListType","type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"limit"}},"type":{"kind":"NamedType","name":{"kind":"Name","value":"Int"}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"cCREQuery"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"accession_prefix"},"value":{"kind":"Variable","name":{"kind":"Name","value":"accession_prefix"}}},{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}},{"kind":"Argument","name":{"kind":"Name","value":"limit"},"value":{"kind":"Variable","name":{"kind":"Name","value":"limit"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"accession"}},{"kind":"Field","name":{"kind":"Name","value":"coordinates"},"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"start"}},{"kind":"Field","name":{"kind":"Name","value":"end"}},{"kind":"Field","name":{"kind":"Name","value":"chromosome"}}]}}]}}]}}]} as unknown as DocumentNode; export const BedIntersectCcre_1Document = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"bedIntersectCCRE_1"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"user_ccres"}},"type":{"kind":"NonNullType","type":{"kind":"ListType","type":{"kind":"NamedType","name":{"kind":"Name","value":"cCRE"}}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"max_ouput_length"}},"type":{"kind":"NamedType","name":{"kind":"Name","value":"Int"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"intersection"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"userCcres"},"value":{"kind":"Variable","name":{"kind":"Name","value":"user_ccres"}}},{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}},{"kind":"Argument","name":{"kind":"Name","value":"maxOutputLength"},"value":{"kind":"Variable","name":{"kind":"Name","value":"max_ouput_length"}}}]}]}}]} as unknown as DocumentNode; export const GetGeneLocationDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"getGeneLocation"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"name"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"gene"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"name"},"value":{"kind":"ListValue","values":[{"kind":"Variable","name":{"kind":"Name","value":"name"}}]}},{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}},{"kind":"Argument","name":{"kind":"Name","value":"version"},"value":{"kind":"IntValue","value":"40"}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"coordinates"},"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"chromosome"}},{"kind":"Field","name":{"kind":"Name","value":"start"}},{"kind":"Field","name":{"kind":"Name","value":"end"}}]}}]}}]}}]} as unknown as DocumentNode; -export const GeneexpressionDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"geneexpression"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"accessions"}},"type":{"kind":"ListType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"gene_id"}},"type":{"kind":"ListType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"gene_dataset"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"accession"},"value":{"kind":"Variable","name":{"kind":"Name","value":"accessions"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"biosample"}},{"kind":"Field","name":{"kind":"Name","value":"tissue"}},{"kind":"Field","name":{"kind":"Name","value":"cell_compartment"}},{"kind":"Field","name":{"kind":"Name","value":"biosample_type"}},{"kind":"Field","name":{"kind":"Name","value":"assay_term_name"}},{"kind":"Field","name":{"kind":"Name","value":"accession"}},{"kind":"Field","name":{"kind":"Name","value":"gene_quantification_files"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"accession"}},{"kind":"Field","name":{"kind":"Name","value":"biorep"}},{"kind":"Field","name":{"kind":"Name","value":"quantifications"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"gene_id_prefix"},"value":{"kind":"Variable","name":{"kind":"Name","value":"gene_id"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"tpm"}},{"kind":"Field","name":{"kind":"Name","value":"file_accession"}},{"kind":"Field","name":{"kind":"Name","value":"fpkm"}}]}}]}}]}}]}}]} as unknown as DocumentNode; +export const GeneexpressionDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"geneexpression"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"gene_id"}},"type":{"kind":"ListType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"gene_dataset"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"processed_assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"biosample"}},{"kind":"Field","name":{"kind":"Name","value":"tissue"}},{"kind":"Field","name":{"kind":"Name","value":"cell_compartment"}},{"kind":"Field","name":{"kind":"Name","value":"biosample_type"}},{"kind":"Field","name":{"kind":"Name","value":"assay_term_name"}},{"kind":"Field","name":{"kind":"Name","value":"accession"}},{"kind":"Field","name":{"kind":"Name","value":"gene_quantification_files"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"accession"}},{"kind":"Field","name":{"kind":"Name","value":"biorep"}},{"kind":"Field","name":{"kind":"Name","value":"quantifications"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"gene_id_prefix"},"value":{"kind":"Variable","name":{"kind":"Name","value":"gene_id"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"tpm"}},{"kind":"Field","name":{"kind":"Name","value":"file_accession"}}]}}]}}]}}]}}]} as unknown as DocumentNode; export const GeneAutocompleteDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"geneAutocomplete"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"name"}},"type":{"kind":"ListType","type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"limit"}},"type":{"kind":"NamedType","name":{"kind":"Name","value":"Int"}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"version"}},"type":{"kind":"NamedType","name":{"kind":"Name","value":"Int"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"gene"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}},{"kind":"Argument","name":{"kind":"Name","value":"name"},"value":{"kind":"Variable","name":{"kind":"Name","value":"name"}}},{"kind":"Argument","name":{"kind":"Name","value":"limit"},"value":{"kind":"Variable","name":{"kind":"Name","value":"limit"}}},{"kind":"Argument","name":{"kind":"Name","value":"version"},"value":{"kind":"Variable","name":{"kind":"Name","value":"version"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"name"}},{"kind":"Field","name":{"kind":"Name","value":"id"}},{"kind":"Field","name":{"kind":"Name","value":"coordinates"},"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"start"}},{"kind":"Field","name":{"kind":"Name","value":"chromosome"}},{"kind":"Field","name":{"kind":"Name","value":"end"}}]}}]}}]}}]} as unknown as DocumentNode; export const GeneOrthologQueryDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"geneOrthologQuery"},"variableDefinitions":[{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"name"}},"type":{"kind":"NonNullType","type":{"kind":"ListType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}},{"kind":"VariableDefinition","variable":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}},"type":{"kind":"NonNullType","type":{"kind":"NamedType","name":{"kind":"Name","value":"String"}}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","alias":{"kind":"Name","value":"geneOrthologQuery"},"name":{"kind":"Name","value":"geneorthologQuery"},"arguments":[{"kind":"Argument","name":{"kind":"Name","value":"name"},"value":{"kind":"Variable","name":{"kind":"Name","value":"name"}}},{"kind":"Argument","name":{"kind":"Name","value":"assembly"},"value":{"kind":"Variable","name":{"kind":"Name","value":"assembly"}}}],"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","alias":{"kind":"Name","value":"humanGene"},"name":{"kind":"Name","value":"external_gene_name"}},{"kind":"Field","alias":{"kind":"Name","value":"mouseGene"},"name":{"kind":"Name","value":"mmusculus_homolog_associated_gene_name"}}]}}]}}]} as unknown as DocumentNode; export const GetAllGwasStudiesDocument = {"kind":"Document","definitions":[{"kind":"OperationDefinition","operation":"query","name":{"kind":"Name","value":"getAllGWASStudies"},"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"getAllGwasStudies"},"selectionSet":{"kind":"SelectionSet","selections":[{"kind":"Field","name":{"kind":"Name","value":"study"}},{"kind":"Field","name":{"kind":"Name","value":"totalldblocks"}},{"kind":"Field","name":{"kind":"Name","value":"author"}},{"kind":"Field","name":{"kind":"Name","value":"pubmedid"}},{"kind":"Field","name":{"kind":"Name","value":"studyname"}}]}}]}}]} as unknown as DocumentNode; diff --git a/screen2.0/yarn.lock b/screen2.0/yarn.lock index 4a9b3664..821fcd4b 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -2,13 +2,13 @@ # Manual changes might be lost - proceed with caution! __metadata: - version: 6 - cacheKey: 8 + version: 8 + cacheKey: 10 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