scRNA-seq_analysis

pipelines/08_violin_plots/violin_plots.R

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+args = commandArgs(trailingOnly=T)
+args = paste(args, collapse = "")
+args = unlist(strsplit(args, ";"))
+if(length(args) != 7){
+  stop('This pipeline requires 7 parameters: seurat.addr, set.ident (from meta.data on which to set identity of cells,
+       type.to.colours (file holding the type to colour key), cell.labels (list of categories or all), plot.width, 
+       plot.height, features.file (name of file that holds the list of genes, should be placed in the resource folder)')
+}
+
+arguments.list = "
+seurat.addr.arg     = args[1]
+set.ident.arg       = args[2]
+type.to.colours.arg = args[3]
+cell.labels.arg     = args[4]
+plot.width.arg      = args[5]   
+plot.height.arg     = args[6]
+features.file.arg   = args[7]
+"
+eval(parse(text = arguments.list))
+
+arguments.list = unlist(strsplit(arguments.list, "\n"))
+arguments.list = arguments.list[!(arguments.list == "")]
+
+for(n in 1:length(arguments.list)){
+  argument = arguments.list[n]
+  argument = gsub(pattern=" ", replacement="", x=argument)
+  argument.name = unlist(strsplit(argument, "="))[1]
+  variable.name = gsub(pattern=".arg", replacement="", argument.name)
+  argument.content = eval(parse(text = argument.name))
+  eval(parse(text = argument.content))
+  if (!exists(variable.name)){
+    stop(sprintf("Argument %s not passed. Stopping ... ", variable.name))
+  }
+}
+
+# create required folders for output and work material
+output_folder = paste("08_violin_plots", seurat.addr, sep = "_")
+c.time = Sys.time()
+c.time = gsub(pattern=" BST", replacement="", x=c.time)
+c.time = gsub(pattern=":", replacement="", x=c.time)
+c.time = gsub(pattern=" ", replacement="", x=c.time)
+c.time = gsub(pattern="-", replacement="", x=c.time)
+c.time = substr(x=c.time, start=3, stop=nchar(c.time))
+output_folder = paste(output_folder, c.time, sep = "_")
+output_folder = file.path("../../output", output_folder)
+dir.create(output_folder)
+
+seurat.addr = file.path("../../data", seurat.addr)
+features.file   = file.path("../../resources", features.file)
+
+features.file = file(features.file, "r")
+features      = readLines(features.file)
+close(features.file)
+
+source("../../tools/bunddle_utils.R")
+
+library(Seurat)
+library(plyr)
+library(dplyr)
+library(reshape)
+library(ggplot2)
+library(RColorBrewer)
+
+#######################################################################################################
+
+print("Loading data ...")
+seurat.obj <- readRDS(seurat.addr)
+print("Data loaded.")
+seurat.obj <- SetAllIdent(object=seurat.obj, id=set.ident)
+print("Data loaded.")
+print("Features present in data:")
+print(table(features %in% rownames(seurat.obj@data)))
+features = intersect(features, rownames(seurat.obj@data))
+
+if(cell.labels == "all"){
+  cell.labels=as.vector(unique(seurat.obj@ident))
+}else{
+  cell.labels = file.path("../../resources", cell.labels)
+  cell.labels.file = file(cell.labels, "r")
+  cell.labels = readLines(cell.labels.file)
+  close(cell.labels.file)
+}
+
+if (!is.na(type.to.colours)){
+  type.to.colours = file.path("../../resources", type.to.colours)
+  type.to.colour <- read.csv(type.to.colours)
+  match.key <- match(cell.labels, type.to.colour$CellTypes)
+  cell.colours <- as.vector(type.to.colour$Colours[match.key])
+}else{
+  cell.colours <- sample(colorRampPalette(brewer.pal(12, "Paired"))(length(cell.labels)))
+}
+
+to.keep = names(seurat.obj@ident)[as.vector(seurat.obj@ident) %in% cell.labels]
+seurat.obj = SubsetData(object=seurat.obj, cells.use=to.keep)
+
+plot_violins <- function(seurat.obj, class.order, class.colours, features){
+  expression.data <- t(as.data.frame(as.matrix(seurat.obj@data[features, ])))
+  expression.data <- melt(expression.data)
+  colnames(expression.data) <- c("CellLabels", "Gene", "Expression")
+  expression.data$CellLabels <- mapvalues(x=expression.data$CellLabels, from=names(seurat.obj@ident), to=as.vector(seurat.obj@ident))
+  expression.data$CellLabels <- factor(as.vector(expression.data$CellLabels), levels = class.order)
+  plot.obj <- ggplot(data=expression.data, aes(x=CellLabels, y = Expression, fill = CellLabels))
+  plot.obj <- plot.obj + geom_violin(scale = 'width')
+  plot.obj <- plot.obj + facet_wrap(~Gene, ncol=1)
+  plot.obj <- plot.obj + theme(axis.text.x = element_text(angle = 90), legend.position = "none")
+  plot.obj <- plot.obj +  scale_fill_manual(values=class.colours)
+  plot.obj
+}
+
+f.name = file.path(output_folder, "features.pdf")
+pdf(f.name, width = plot.width, height = plot.height)
+print(plot_violins(seurat.obj, class.order=cell.labels, class.colours=cell.colours, features))
+dev.off()
+
+print("Ended beautifully ... ")

pipelines/08_violin_plots/violin_plots.sh

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+#!/bin/bash
+
+#$ -cwd
+#$ -N violin_plots
+#$ -V
+#$ -l h_rt=47:59:59
+#$ -l h_vmem=200G
+
+if [ "$#" -ne 1 ]; then
+    echo "Illegal number of parameters"
+    exit 1
+fi
+
+Rscript violin_plots.R $1
+
+echo "End on `date`"