Merge pull request #165 from weng-lab/atacdata

added atac data

screen2.0/src/app/applets/differential-gene-expression/queries.ts

@@ -29,6 +29,8 @@ export const ZSCORE_QUERY = gql`
     $gene_pc_end: Int
     $rank_ctcf_end: Float!
     $rank_ctcf_start: Float!
+    $rank_atac_end: Float!
+    $rank_atac_start: Float!
     $rank_dnase_end: Float!
     $rank_dnase_start: Float!
     $rank_enhancer_end: Float!
@@ -51,6 +53,8 @@ export const ZSCORE_QUERY = gql`
       gene_pc_end: $gene_pc_end
       rank_ctcf_end: $rank_ctcf_end
       rank_ctcf_start: $rank_ctcf_start
+      rank_atac_end: $rank_atac_end
+      rank_atac_start: $rank_atac_start
       rank_dnase_end: $rank_dnase_end
       rank_dnase_start: $rank_dnase_start
       rank_enhancer_end: $rank_enhancer_end

screen2.0/src/app/search/fetchRows.ts

@@ -52,10 +52,11 @@ export async function generateRows(QueryResult: ApolloQueryResult<any>, biosampl
         end: (currentElement.start + currentElement.len).toLocaleString("en-US"),
         dnase: biosample ? currentElement.ctspecific.dnase_zscore : currentElement.dnase_zscore,
         //Need to get this data still from somewhere
-        atac: "TBD",
+
         h3k4me3: biosample ? currentElement.ctspecific.h3k4me3_zscore : currentElement.promoter_zscore,
         h3k27ac: biosample ? currentElement.ctspecific.h3k27ac_zscore : currentElement.enhancer_zscore,
         ctcf: biosample ? currentElement.ctspecific.ctcf_zscore : currentElement.ctcf_zscore,
+        atac: biosample ? currentElement.ctspecific.atac_zscore : currentElement.atac_zscore,
         linkedGenes: { distancePC: currentElement.genesallpc.pc.intersecting_genes, distanceAll: currentElement.genesallpc.all.intersecting_genes, CTCF_ChIAPET: [], RNAPII_ChIAPET: [] },
         conservationData: {mammals: currentElement.mammals, primates: currentElement.primates, vertebrates: currentElement.vertebrates}
       })

screen2.0/src/app/search/search-helpers.ts

@@ -44,6 +44,7 @@ function passesChromatinFilter(currentElement: cCREData, biosample: string | nul
   const h3k4me3 = biosample ? currentElement.ctspecific.h3k4me3_zscore : currentElement.promoter_zscore
   const h3k27ac = biosample ? currentElement.ctspecific.h3k27ac_zscore : currentElement.enhancer_zscore
   const ctcf = biosample ? currentElement.ctspecific.ctcf_zscore : currentElement.ctcf_zscore
+  const atac = biosample ? currentElement.ctspecific.atac_zscore : currentElement.atac_zscore
   if (
     mainQueryParams.dnase_s <= dnase &&
     dnase <= mainQueryParams.dnase_e &&
@@ -52,7 +53,7 @@ function passesChromatinFilter(currentElement: cCREData, biosample: string | nul
     mainQueryParams.h3k27ac_s <= h3k27ac &&
     h3k27ac <= mainQueryParams.h3k27ac_e &&
     mainQueryParams.ctcf_s <= ctcf &&
-    ctcf <= mainQueryParams.ctcf_e
+    ctcf <= mainQueryParams.ctcf_e 
   ) {
     return true
   } else return false

screen2.0/src/app/search/types.ts

@@ -11,7 +11,7 @@ export type cCREData = {
   start: number
   len: number
   dnase_zscore?: number
-  atac: string
+  atac_zscore?: number  
   promoter_zscore?: number
   enhancer_zscore?: number
   ctcf_zscore?: number
@@ -24,6 +24,7 @@ export type cCREData = {
     h3k4me3_zscore?: number
     h3k27ac_zscore?: number
     ctcf_zscore?: number
+    atac_zscore?: number
   }
   genesallpc: {
     all: {
@@ -59,6 +60,8 @@ export type MainQueryParams = {
   h3k4me3_e?: number
   h3k27ac_s?: number
   h3k27ac_e?: number
+  atac_s?: number
+  atac_e?: number
   vert_s?: number
   vert_e?: number
   mamm_s?: number
@@ -132,7 +135,7 @@ export type MainResultTableRow = {
   start: string
   end: string
   dnase?: number
-  atac: string
+  atac?: number
   h3k4me3?: number
   h3k27ac?: number
   ctcf?: number

screen2.0/src/common/components/MainResultsTable.tsx

@@ -41,14 +41,9 @@ function MainResultsTable(props: MainResultsTableProps) {
       {
         header: "End",
         value: (row: { end: string }) => row.end,
-      },
-      {
-        header: "ATAC",
-        //Atac is a string because the data does not exist and is "TBD" for now
-        value: (row: { atac: string }) => row.atac,
-      },
+      }
     ]
-
+   
     if (props.rows[0] && props.rows[0].dnase !== null) {
       cols.push({
         header: "DNase",
@@ -73,7 +68,12 @@ function MainResultsTable(props: MainResultsTableProps) {
         value: (row) => (row.h3k4me3 && row.h3k4me3.toFixed(2)) || 0,
       })
     }
-
+    if (props.rows[0] && props.rows[0].atac !== null) {
+      cols.push({
+        header: "ATAC",
+        value: (row) => (row.atac && row.atac.toFixed(2)) || 0,
+      })
+    }
     //Whenever the state of the checkboxes conflicts with the state of the main component, it triggers a rerender
     cols.push({
       header: "Linked\u00A0Genes\u00A0(Distance)",
@@ -207,14 +207,14 @@ function MainResultsTable(props: MainResultsTableProps) {
       <LoadingMessage />
       :
       <DataTable
-        key={props.rows[0] && props.rows[0].dnase + props.rows[0].ctcf + props.rows[0].h3k27ac + props.rows[0].h3k4me3 + columns.toString() + distance + CTCF_ChIAPET + RNAPII_ChIAPET}
+        key={props.rows[0] && props.rows[0].dnase + props.rows[0].ctcf + props.rows[0].h3k27ac + props.rows[0].h3k4me3 +  props.rows[0].atac  + columns.toString() + distance + CTCF_ChIAPET + RNAPII_ChIAPET}
         rows={props.rows}
         columns={columns(setDistance, setCTCF_ChIAPET, setRNAPII_ChIAPET)}
         itemsPerPage={props.itemsPerPage}
         searchable
         onRowClick={props.onRowClick}
         tableTitle={props.tableTitle}
-        sortColumn={6}
+        sortColumn={5}
         showMoreColumns
         noOfDefaultColumns={11}
         titleHoverInfo={props.titleHoverInfo}

screen2.0/src/common/lib/queries.ts

@@ -27,6 +27,8 @@ query ccreSearchQuery(
   $rank_enhancer_start: Float!
   $rank_promoter_end: Float!
   $rank_promoter_start: Float!
+  $rank_atac_end: Float!
+  $rank_atac_start: Float!
   $mammals_min: Float
   $mammals_max: Float
   $vertebrates_min: Float
@@ -48,6 +50,8 @@ query ccreSearchQuery(
     gene_all_end: $gene_all_end
     gene_pc_start: $gene_pc_start
     gene_pc_end: $gene_pc_end
+    rank_atac_end: $rank_atac_end
+    rank_atac_start: $rank_atac_start
     rank_ctcf_end: $rank_ctcf_end
     rank_ctcf_start: $rank_ctcf_start
     rank_dnase_end: $rank_dnase_end
@@ -76,12 +80,14 @@ query ccreSearchQuery(
     dnase_zscore
     enhancer_zscore
     promoter_zscore
+    atac_zscore
     ctspecific {
       ct
       dnase_zscore
       h3k4me3_zscore
       h3k27ac_zscore
       ctcf_zscore
+      atac_zscore
     }
     info {
       accession
@@ -211,6 +217,8 @@ function cCRE_QUERY_VARIABLES(assembly: string, chromosome: string, start: numbe
     gene_pc_end: 5000000,
     rank_dnase_start: -10,
     rank_dnase_end: 10,
+    rank_atac_start: -10,
+    rank_atac_end: 10,
     rank_promoter_start: -10,
     rank_promoter_end: 10,
     rank_enhancer_start: -10,