From e3b547b013b81f118a68a0bec7f28f7193ba8664 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 17:26:29 +1000 Subject: [PATCH 1/9] Updates --- NAMESPACE | 2 +- R/package.check.R | 1 + R/package.install.R | 133 ++++++++++++++++++++++++++++------------- R/package.load.R | 1 + man/package.install.Rd | 2 + 5 files changed, 97 insertions(+), 42 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 40c617ba..dc0d6f56 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,8 +12,8 @@ export(do.align) export(do.asinh) export(do.calculate.area) export(do.clip) -export(do.create.outlines) export(do.combine.cols) +export(do.create.outlines) export(do.embed.columns) export(do.extract) export(do.extract.cell.dat) diff --git a/R/package.check.R b/R/package.check.R index 8dbaf0ee..70bc9b56 100755 --- a/R/package.check.R +++ b/R/package.check.R @@ -53,5 +53,6 @@ package.check <- function(type = "general"){ if(!is.element('sf', installed.packages()[,1])) message('sf is required for SPATIAL analysis but is not installed') if(!is.element('stars', installed.packages()[,1])) message('stars is required for SPATIAL analysis but is not installed') if(!is.element('qs', installed.packages()[,1])) message('qs is required for SPATIAL analysis but is not installed') + if(!is.element('s2', installed.packages()[,1])) message('s2 is required for SPATIAL analysis but is not installed') } } diff --git a/R/package.install.R b/R/package.install.R index a45fe03b..7f5036bb 100755 --- a/R/package.install.R +++ b/R/package.install.R @@ -5,6 +5,7 @@ #' @return returns an error message if one of the common use packages are not installed. Proceeds in order of package importance, and only the first error message encountered will be returned. #' #' @param type DEFAULT = "general". If "general", then checks for the packages required for general Spectre usage. If "spatial", then checks for additional packages required for spatial analysis. +#' @param update DEFAULT = FALSE. If FALSE, will only install packages that are not already installed -- no updates of packages will be performed. If TRUE, will install and update packages. #' #' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au} #' @@ -18,49 +19,99 @@ #' #' @export -package.install <- function(type = 'general'){ +package.install <- function(type = 'general', update = FALSE){ - if(!require('data.table')) {install.packages('data.table')} - if(!require('plyr')) {install.packages('plyr')} - if(!require('dplyr')) {install.packages('dplyr')} - if(!require('tidyr')) {install.packages('tidyr')} - if(!require('rstudioapi')) {install.packages('rstudioapi')} - if(!require('Rtsne')) {install.packages('Rtsne')} - if(!require('umap')) {install.packages('umap')} - if(!require('ggplot2')) {install.packages('ggplot2')} - if(!require('ggthemes')) {install.packages('ggthemes')} - if(!require('scales')) {install.packages('scales')} - if(!require('colorRamps')) {install.packages('colorRamps')} - if(!require('RColorBrewer')) {install.packages('')} - if(!require('gridExtra')) {install.packages('gridExtra')} - if(!require('ggpointdensity')) {install.packages('ggpointdensity')} - if(!require('pheatmap')) {install.packages('pheatmap')} - if(!require('ggpubr')) {install.packages('ggpubr')} - if(!require('factoextra')) {install.packages('factoextra')} - if(!require('reticulate')) {install.packages('reticulate')} - if(!require('caret')) {install.packages('caret')} - if(!require('class')) {install.packages('class')} - - ## Install BiocManager to download packages from Bioconductor - if (!requireNamespace("BiocManager", quietly = TRUE)) - install.packages("BiocManager") - - ## Download additional BioConductor packages - if(!require('flowCore')) {BiocManager::install('flowCore')} - if(!require('Biobase')) {BiocManager::install('Biobase')} - if(!require('flowViz')) {BiocManager::install('flowViz')} - if(!require('FlowSOM')) {BiocManager::install('FlowSOM')} + ## Update = FALSE + if(isFALSE(update)){ + if(!require('data.table')) {install.packages('data.table')} + if(!require('plyr')) {install.packages('plyr')} + if(!require('dplyr')) {install.packages('dplyr')} + if(!require('tidyr')) {install.packages('tidyr')} + if(!require('rstudioapi')) {install.packages('rstudioapi')} + if(!require('Rtsne')) {install.packages('Rtsne')} + if(!require('umap')) {install.packages('umap')} + if(!require('ggplot2')) {install.packages('ggplot2')} + if(!require('ggthemes')) {install.packages('ggthemes')} + if(!require('scales')) {install.packages('scales')} + if(!require('colorRamps')) {install.packages('colorRamps')} + if(!require('RColorBrewer')) {install.packages('')} + if(!require('gridExtra')) {install.packages('gridExtra')} + if(!require('ggpointdensity')) {install.packages('ggpointdensity')} + if(!require('pheatmap')) {install.packages('pheatmap')} + if(!require('ggpubr')) {install.packages('ggpubr')} + if(!require('factoextra')) {install.packages('factoextra')} + if(!require('reticulate')) {install.packages('reticulate')} + if(!require('caret')) {install.packages('caret')} + if(!require('class')) {install.packages('class')} + + ## Install BiocManager to download packages from Bioconductor + if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + + ## Download additional BioConductor packages + if(!require('flowCore')) {BiocManager::install('flowCore')} + if(!require('Biobase')) {BiocManager::install('Biobase')} + if(!require('flowViz')) {BiocManager::install('flowViz')} + if(!require('FlowSOM')) {BiocManager::install('FlowSOM')} + + if(type == "spatial"){ + if(!require('raster')) {install.packages('raster')} + if(!require('tiff')) {install.packages('tiff')} + if(!require('rgeos')) {install.packages('rgeos')} + if(!require('exactextractr')) {install.packages('exactextractr')} + if(!require('sp')) {install.packages('sp')} + if(!require('sf')) {install.packages('sf')} + if(!require('stars')) {install.packages('stars')} + if(!require('qs')) {install.packages('qs')} + if(!require('s2')) {install.packages('s2')} + } + } + + ## Update = TRUE + if(isTRUE(update)){ + install.packages('data.table') + install.packages('plyr') + install.packages('dplyr') + install.packages('tidyr') + install.packages('rstudioapi') + install.packages('Rtsne') + install.packages('umap') + install.packages('ggplot2') + install.packages('ggthemes') + install.packages('scales') + install.packages('colorRamps') + install.packages('') + install.packages('gridExtra') + install.packages('ggpointdensity') + install.packages('pheatmap') + install.packages('ggpubr') + install.packages('factoextra') + install.packages('reticulate') + install.packages('caret') + install.packages('class') + + ## Install BiocManager to download packages from Bioconductor + install.packages("BiocManager") + + ## Download additional BioConductor packages + BiocManager::install('flowCore') + BiocManager::install('Biobase') + BiocManager::install('flowViz') + BiocManager::install('FlowSOM') + + if(type == "spatial"){ + install.packages('raster') + install.packages('tiff') + install.packages('rgeos') + install.packages('exactextractr') + install.packages('sp') + install.packages('sf') + install.packages('stars') + install.packages('qs') + install.packages('s2') + } + } - if(type == "spatial"){ - if(!require('raster')) {install.packages('raster')} - if(!require('tiff')) {install.packages('tiff')} - if(!require('rgeos')) {install.packages('rgeos')} - if(!require('exactextractr')) {install.packages('exactextractr')} - if(!require('sp')) {install.packages('sp')} - if(!require('sf')) {install.packages('sf')} - if(!require('stars')) {install.packages('stars')} - if(!require('qs')) {install.packages('qs')} - } } diff --git a/R/package.load.R b/R/package.load.R index 3f5fc7ad..d505cf14 100755 --- a/R/package.load.R +++ b/R/package.load.R @@ -55,5 +55,6 @@ package.load <- function(type = "general"){ require('sf') require('stars') require('qs') + require('s2') } } diff --git a/man/package.install.Rd b/man/package.install.Rd index f7b5f9f3..69a002cc 100755 --- a/man/package.install.Rd +++ b/man/package.install.Rd @@ -8,6 +8,8 @@ See \url{https://sydneycytometry.org.au/spectre} for usage instructions and vign } \arguments{ \item{type}{DEFAULT = "general". If "general", then checks for the packages required for general Spectre usage. If "spatial", then checks for additional packages required for spatial analysis.} + +\item{update}{DEFAULT = FALSE. If FALSE, will only install packages that are not already installed -- no updates of packages will be performed. If TRUE, will install and update packages.} } \value{ returns an error message if one of the common use packages are not installed. Proceeds in order of package importance, and only the first error message encountered will be returned. From a68a47a41a2366a0d42935b076654fcec755830b Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 17:49:39 +1000 Subject: [PATCH 2/9] Update DESCRIPTION --- DESCRIPTION | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 9aae58b1..d5d687a0 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,6 +9,11 @@ Depends: R (>= 3.6.0) License: MIT Licence Encoding: UTF-8 LazyData: true +biocViews: + flowCore, + Biobase, + flowViz, + FlowSOM, Imports: devtools, plyr, From c3c231fc9b273657f14b58dfa77be16610494c87 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 17:52:38 +1000 Subject: [PATCH 3/9] Updates --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index d5d687a0..0b15025f 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,6 +16,7 @@ biocViews: FlowSOM, Imports: devtools, + BiocManager, plyr, dplyr, data.table, From dfc55efff4be52bcb0de27d6bf2b22d425aa4177 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 18:36:43 +1000 Subject: [PATCH 4/9] Updates --- DESCRIPTION | 8 +- R/package.check.R | 200 ++++++++++++++++++++++++++++++++++++++-------- 2 files changed, 172 insertions(+), 36 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0b15025f..3b59cd9e 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,10 +10,6 @@ License: MIT Licence Encoding: UTF-8 LazyData: true biocViews: - flowCore, - Biobase, - flowViz, - FlowSOM, Imports: devtools, BiocManager, @@ -55,5 +51,9 @@ Imports: s2, exactextractr, Suggests: + flowCore, + Biobase, + flowViz, + FlowSOM, RoxygenNote: 7.1.1 Roxygen: list(markdown = TRUE) diff --git a/R/package.check.R b/R/package.check.R index 70bc9b56..01b4235e 100755 --- a/R/package.check.R +++ b/R/package.check.R @@ -19,40 +19,176 @@ package.check <- function(type = "general"){ - if(!is.element('data.table', installed.packages()[,1])) message('data.table is required but not installed') - if(!is.element('plyr', installed.packages()[,1])) message('plyr is required but not installed') - if(!is.element('dplyr', installed.packages()[,1])) message('dplyr is required but not installed') - if(!is.element('tidyr', installed.packages()[,1])) message('tidyr is required but not installed') - if(!is.element('rstudioapi', installed.packages()[,1])) message('rstudioapi is required but not installed') - if(!is.element('Rtsne', installed.packages()[,1])) message('Rtsne is required but not installed') - if(!is.element('umap', installed.packages()[,1])) message('umap is required but not installed') - if(!is.element('reticulate', installed.packages()[,1])) message('reticulate is required but not installed') - if(!is.element('ggplot2', installed.packages()[,1])) message('ggplot2 is required but not installed') - if(!is.element('ggthemes', installed.packages()[,1])) message('ggthemes is required but not installed') - if(!is.element('scales', installed.packages()[,1])) message('scales is required but not installed') - if(!is.element('colorRamps', installed.packages()[,1])) message('colorRamps is required but not installed') - if(!is.element('RColorBrewer', installed.packages()[,1])) message('RColorBrewer is required but not installed') - if(!is.element('gridExtra', installed.packages()[,1])) message('gridExtra is required but not installed') - if(!is.element('ggpointdensity', installed.packages()[,1])) message('ggpointdensity is required but not installed') - if(!is.element('pheatmap', installed.packages()[,1])) message('ggpointdensity is required but not installed') - if(!is.element('ggpubr', installed.packages()[,1])) message('ggpointdensity is required but not installed') - if(!is.element('caret', installed.packages()[,1])) message('caret is required for machine learning analysis but is not installed') - if(!is.element('class', installed.packages()[,1])) message('class is required for machine learning analysis but is not installed') + res.list <- list() - if(!is.element('flowCore', installed.packages()[,1])) message('flowCore is required but not installed. Please install from BioConductor.') - if(!is.element('Biobase', installed.packages()[,1])) message('Biobase is required but not installed. Please install from BioConductor.') - if(!is.element('flowViz', installed.packages()[,1])) message('flowViz is required but not installed. Please install from BioConductor.') - if(!is.element('FlowSOM', installed.packages()[,1])) message('FlowSOM is required but not installed. Please install from BioConductor.') + if(!is.element('data.table', installed.packages()[,1])){ + message('data.table is required but not installed') + res.list[['data.table']] <- 'data.table' + } + + if(!is.element('plyr', installed.packages()[,1])) { + message('plyr is required but not installed') + res.list[['plyr']] <- 'plyr' + } + + if(!is.element('dplyr', installed.packages()[,1])) { + message('dplyr is required but not installed') + res.list[['data.table']] <- 'data.table' + } + + if(!is.element('tidyr', installed.packages()[,1])) { + message('tidyr is required but not installed') + res.list[['tidyr']] <- 'tidyr' + } + + if(!is.element('rstudioapi', installed.packages()[,1])) { + message('rstudioapi is required but not installed') + res.list[['rstudioapi']] <- 'rstudioapi' + } + + if(!is.element('Rtsne', installed.packages()[,1])) { + message('Rtsne is required but not installed') + res.list[['Rtsne']] <- 'Rtsne' + } + + if(!is.element('umap', installed.packages()[,1])) { + message('umap is required but not installed') + res.list[['umap']] <- 'umap' + } + + if(!is.element('reticulate', installed.packages()[,1])) { + message('reticulate is required but not installed') + res.list[['reticulate']] <- 'reticulate' + } + + if(!is.element('ggplot2', installed.packages()[,1])) { + message('ggplot2 is required but not installed') + res.list[['ggplot2']] <- 'ggplot2' + } + + if(!is.element('ggthemes', installed.packages()[,1])) { + message('ggthemes is required but not installed') + res.list[['ggthemes']] <- 'ggthemes' + } + + if(!is.element('scales', installed.packages()[,1])) { + message('scales is required but not installed') + res.list[['scales']] <- 'scales' + } + + if(!is.element('colorRamps', installed.packages()[,1])) { + message('colorRamps is required but not installed') + res.list[['colorRamps']] <- 'colorRamps' + } + + if(!is.element('RColorBrewer', installed.packages()[,1])) { + message('RColorBrewer is required but not installed') + res.list[['RColorBrewer']] <- 'RColorBrewer' + } + + if(!is.element('gridExtra', installed.packages()[,1])) { + message('gridExtra is required but not installed') + res.list[['gridExtra']] <- 'gridExtra' + } + + if(!is.element('ggpointdensity', installed.packages()[,1])) { + message('ggpointdensity is required but not installed') + res.list[['ggpointdensity']] <- 'ggpointdensity' + } + + if(!is.element('pheatmap', installed.packages()[,1])) { + message('pheatmap is required but not installed') + res.list[['pheatmap']] <- 'pheatmap' + } + + if(!is.element('ggpubr', installed.packages()[,1])) { + message('ggpubr is required but not installed') + res.list[['ggpubr']] <- 'ggpubr' + } + + if(!is.element('caret', installed.packages()[,1])) { + message('caret is required for machine learning analysis but is not installed') + res.list[['caret']] <- 'caret' + } + + if(!is.element('class', installed.packages()[,1])) { + message('class is required for machine learning analysis but is not installed') + res.list[['class']] <- 'class' + } + + if(!is.element('flowCore', installed.packages()[,1])) { + message('flowCore is required but not installed. Please install from BioConductor.') + res.list[['flowCore']] <- 'flowCore' + } + + if(!is.element('Biobase', installed.packages()[,1])) { + message('Biobase is required but not installed. Please install from BioConductor.') + res.list[['Biobase']] <- 'Biobase' + } + + if(!is.element('flowViz', installed.packages()[,1])) { + message('flowViz is required but not installed. Please install from BioConductor.') + res.list[['flowViz']] <- 'flowViz' + } + + if(!is.element('FlowSOM', installed.packages()[,1])) { + message('FlowSOM is required but not installed. Please install from BioConductor.') + res.list[['FlowSOM']] <- 'FlowSOM' + } + if(type == "spatial"){ - if(!is.element('raster', installed.packages()[,1])) message('raster is required for SPATIAL analysis but is not installed') - if(!is.element('tiff', installed.packages()[,1])) message('tiff is required for SPATIAL analysis but is not installed') - if(!is.element('rgeos', installed.packages()[,1])) message('rgeos is required for SPATIAL analysis but is not installed') - if(!is.element('exactextractr', installed.packages()[,1])) message('exactextractr is required for SPATIAL analysis but is not installed') - if(!is.element('sp', installed.packages()[,1])) message('sp is required for SPATIAL analysis but is not installed') - if(!is.element('sf', installed.packages()[,1])) message('sf is required for SPATIAL analysis but is not installed') - if(!is.element('stars', installed.packages()[,1])) message('stars is required for SPATIAL analysis but is not installed') - if(!is.element('qs', installed.packages()[,1])) message('qs is required for SPATIAL analysis but is not installed') - if(!is.element('s2', installed.packages()[,1])) message('s2 is required for SPATIAL analysis but is not installed') + if(!is.element('raster', installed.packages()[,1])) { + message('raster is required for SPATIAL analysis but is not installed') + res.list[['raster']] <- 'raster' + } + + if(!is.element('tiff', installed.packages()[,1])) { + message('tiff is required for SPATIAL analysis but is not installed') + res.list[['tiff']] <- 'tiff' + } + + if(!is.element('rgeos', installed.packages()[,1])) { + message('rgeos is required for SPATIAL analysis but is not installed') + res.list[['rgeos']] <- 'rgeos' + } + + if(!is.element('exactextractr', installed.packages()[,1])) { + message('exactextractr is required for SPATIAL analysis but is not installed') + res.list[['exactextractr']] <- 'exactextractr' + } + + if(!is.element('sp', installed.packages()[,1])) { + message('sp is required for SPATIAL analysis but is not installed') + res.list[['sp']] <- 'sp' + } + + if(!is.element('sf', installed.packages()[,1])) { + message('sf is required for SPATIAL analysis but is not installed') + res.list[['sf']] <- 'sf' + } + + if(!is.element('stars', installed.packages()[,1])) { + message('stars is required for SPATIAL analysis but is not installed') + res.list[['stars']] <- 'stars' + } + + if(!is.element('qs', installed.packages()[,1])) { + message('qs is required for SPATIAL analysis but is not installed') + res.list[['qs']] <- 'qs' + } + + if(!is.element('s2', installed.packages()[,1])) { + message('s2 is required for SPATIAL analysis but is not installed') + res.list[['s2']] <- 's2' + } } + + + ### Final message + + if(length(res.list) == 0){ + message("All packages successfully installed") + } + } From 5f411a2c0ec0073efa19490ed0a0ba64bf178af3 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 18:48:18 +1000 Subject: [PATCH 5/9] Updates --- DESCRIPTION | 15 +++++++++++---- R/prep.cytonorm.R | 2 +- R/run.cytonorm.R | 13 +++++++++---- R/run.flowsom.R | 4 ++-- R/train.cytonorm.R | 10 ++++++++-- 5 files changed, 31 insertions(+), 13 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3b59cd9e..171eba6b 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,17 @@ Package: Spectre Type: Package -Title: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. -Version: 0.5.1 -Author: Thomas Ashhurst, Felix Marsh-Wakefield, Givanna Putri +Version: 0.5.2 +Date: 2021-06-18 +Title: High-dimensional cytometry and imaging analysis. +Description A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. +Authors@R: c( + person(given = "Thomas", family = "Ashhurst", email = "thomas.ashhurst@sydney.edu.au", role = "ctb"), + person(given = "Felix", family = "Marsh-Wakefield", email = "felix.marsh-wakefield@sydney.edu.au", role = "ctb"), + person(given = "Givanna", family = "Putri", email = "givanna.putri@sydney.edu.au", role = "ctb") + ) +URL: https://github.com/ImmuneDynamics/Spectre +BugReports: https://github.com/ImmuneDynamics/Spectre/issues Maintainer: Thomas Ashhurst -Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. Depends: R (>= 3.6.0) License: MIT Licence Encoding: UTF-8 diff --git a/R/prep.cytonorm.R b/R/prep.cytonorm.R index 92cef765..fcd0077e 100755 --- a/R/prep.cytonorm.R +++ b/R/prep.cytonorm.R @@ -54,7 +54,7 @@ prep.cytonorm <- function(dat, require(Spectre) require(data.table) require(CytoNorm) - require(flowCore) + # require(flowCore) require(Biobase) ### Directory setup diff --git a/R/run.cytonorm.R b/R/run.cytonorm.R index 1c132276..4c8bccd2 100755 --- a/R/run.cytonorm.R +++ b/R/run.cytonorm.R @@ -168,7 +168,8 @@ run.cytonorm <- function(dat, dir.create("tmp-target") setwd("tmp-target") - ff <- flowCore::read.FCS(file) + # ff <- flowCore::read.FCS(file) + ff <- read.FCS(file) setwd(dir) dir.create("tmp-target", showWarnings = FALSE) @@ -188,8 +189,9 @@ run.cytonorm <- function(dat, paste0(gsub("[:/]","_",file), "_fsom", cluster, ".fcs")) suppressWarnings( - flowCore::write.FCS(ff[cellClusterIDs[[file]] == cluster], - file = f) + # flowCore::write.FCS(ff[cellClusterIDs[[file]] == cluster], + # file = f) + write.FCS(ff[cellClusterIDs[[file]] == cluster], file = f) ) } } @@ -228,7 +230,10 @@ run.cytonorm <- function(dat, for(i in cluster.files){ # i <- cluster.files[[1]] - temp <- flowCore::read.FCS(i) + + #temp <- flowCore::read.FCS(i) + temp <- read.FCS(i) + dt <- as.data.table(temp@exprs) mc <- sub(".*.fcs_", "", i) diff --git a/R/run.flowsom.R b/R/run.flowsom.R index 952cb4ee..c152f200 100755 --- a/R/run.flowsom.R +++ b/R/run.flowsom.R @@ -53,7 +53,7 @@ run.flowsom <- function(dat, ### Require packages require(Spectre) - require(flowCore) + # require(flowCore) require(Biobase) require(FlowSOM) require(data.table) @@ -91,7 +91,7 @@ run.flowsom <- function(dat, exprs=as.matrix(dat), # in order to create a flow frame, data needs to be read as matrix parameters=Biobase::AnnotatedDataFrame(metadata)) - head(flowCore::exprs(dat.ff)) + #head(flowCore::exprs(dat.ff)) dat_FlowSOM <- dat.ff rm(dat) diff --git a/R/train.cytonorm.R b/R/train.cytonorm.R index 93543139..31777a0e 100755 --- a/R/train.cytonorm.R +++ b/R/train.cytonorm.R @@ -53,7 +53,7 @@ train.cytonorm <- function(model, require(Spectre) require(data.table) require(CytoNorm) - require(flowCore) + # require(flowCore) require(Biobase) ### Check the alignment model object @@ -151,12 +151,18 @@ if(method == 'cytonorm'){ if (sum(FlowSOM::GetMetaclusters(fsom_file, model$fsom$metaclustering) == cluster) > 0) { suppressWarnings( - flowCore::write.FCS( + write.FCS( file.ff[cellClusterIDs == cluster,], file=file.path(getwd(), ##### #outputDir, paste0(gsub("[:/]","_",file), "_fsom",cluster,".fcs")))) + # flowCore::write.FCS( + # file.ff[cellClusterIDs == cluster,], + # file=file.path(getwd(), ##### + # #outputDir, + # paste0(gsub("[:/]","_",file), + # "_fsom",cluster,".fcs")))) } } } From aecb76b1cbbf122fb695c6d906a5bbbf97f2dd41 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 18:50:14 +1000 Subject: [PATCH 6/9] Update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 171eba6b..bd12bf4c 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Version: 0.5.2 Date: 2021-06-18 Title: High-dimensional cytometry and imaging analysis. -Description A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. +Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. Authors@R: c( person(given = "Thomas", family = "Ashhurst", email = "thomas.ashhurst@sydney.edu.au", role = "ctb"), person(given = "Felix", family = "Marsh-Wakefield", email = "felix.marsh-wakefield@sydney.edu.au", role = "ctb"), From 11229757228ed52431e4bcb5336a0f00ecc32c69 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 18:53:07 +1000 Subject: [PATCH 7/9] Updates --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bd12bf4c..d0d9ac6b 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Date: 2021-06-18 Title: High-dimensional cytometry and imaging analysis. Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. Authors@R: c( - person(given = "Thomas", family = "Ashhurst", email = "thomas.ashhurst@sydney.edu.au", role = "ctb"), + person(given = "Thomas", family = "Ashhurst", email = "thomas.ashhurst@sydney.edu.au", role = c("aut", "cre")), person(given = "Felix", family = "Marsh-Wakefield", email = "felix.marsh-wakefield@sydney.edu.au", role = "ctb"), person(given = "Givanna", family = "Putri", email = "givanna.putri@sydney.edu.au", role = "ctb") ) From 108a9fd9fbf72bc964db5f7fc9b25daafc269d88 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 19:08:14 +1000 Subject: [PATCH 8/9] Update DESCRIPTION --- DESCRIPTION | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d0d9ac6b..7c077271 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,8 +6,8 @@ Title: High-dimensional cytometry and imaging analysis. Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. Authors@R: c( person(given = "Thomas", family = "Ashhurst", email = "thomas.ashhurst@sydney.edu.au", role = c("aut", "cre")), - person(given = "Felix", family = "Marsh-Wakefield", email = "felix.marsh-wakefield@sydney.edu.au", role = "ctb"), - person(given = "Givanna", family = "Putri", email = "givanna.putri@sydney.edu.au", role = "ctb") + person(given = "Felix", family = "Marsh-Wakefield", email = "felix.marsh-wakefield@sydney.edu.au", role = "aut"), + person(given = "Givanna", family = "Putri", email = "givanna.putri@sydney.edu.au", role = "aut") ) URL: https://github.com/ImmuneDynamics/Spectre BugReports: https://github.com/ImmuneDynamics/Spectre/issues @@ -18,6 +18,10 @@ Encoding: UTF-8 LazyData: true biocViews: Imports: + flowCore, + Biobase, + flowViz, + FlowSOM, devtools, BiocManager, plyr, @@ -57,10 +61,5 @@ Imports: qs, s2, exactextractr, -Suggests: - flowCore, - Biobase, - flowViz, - FlowSOM, RoxygenNote: 7.1.1 Roxygen: list(markdown = TRUE) From 72a5f716fbb46fc6c47fdee27c53244ab8c78044 Mon Sep 17 00:00:00 2001 From: "tom.ashhurst" Date: Fri, 18 Jun 2021 19:16:43 +1000 Subject: [PATCH 9/9] Updates --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7c077271..56030b46 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ Depends: R (>= 3.6.0) License: MIT Licence Encoding: UTF-8 LazyData: true -biocViews: +biocViews: flowCore Imports: flowCore, Biobase,