Prevent crashes in barcode selection, set up for stats generation (a5109444) · Commits · github_fork / ZUMIs

barcodeIDFUN.R

+36 −21

Original line number	Diff line number	Diff line
		@@ -47,8 +47,13 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){
		cut <- .FindBCcut(bccount)
		nkeep<-bccount[n>=cut][,list(s=.N)]
		if(nkeep<10){
		print("Attention! Adaptive BC selection gave < 10 cells so I will now use top 100 cells!")
		print("Warning! Adaptive BC selection gave < 10 cells so I will try to use top 100 cells!")
		if(nrow(bccount)<100){
		print("Less than 100 barcodes present, will continue with all barcodes...")
		bccount[1:nrow(bccount),keep:=TRUE]
		}else{
		bccount[1:100,keep:=TRUE]
		}
		}else{
		bccount[n>=cut,keep:=TRUE]
		print(paste(nkeep," barcodes detected.",sep=""))
		@@ -80,7 +85,18 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){
		return( bccount[keep==TRUE,XC] )
		}
		.cellBarcode_number <- function( bccount, bcNumber){
		if(bcNumber <= nrow(bccount)){
		bccount[1:bcNumber,keep:=TRUE]
		}else{
		print("Warning! The data contains fewer barcodes than requested so I will try to use top 100 cells!")
		if(nrow(bccount)<100){
		print("Less than 100 barcodes present, will continue with all barcodes...")
		bccount[1:nrow(bccount),keep:=TRUE]
		}else{
		bccount[1:100,keep:=TRUE]
		}
		}

		return(bccount[keep==TRUE,XC])
		}
		.cellBarcode_known <- function( bccount, bcfile ){
		@@ -137,4 +153,3 @@ plotReadCountSelection<-function(bccount , mads, filename){
		abline(h=MAD_up,col="red")
		dev.off()
		}

+1 −0

Original line number	Diff line number	Diff line
		@@ -156,6 +156,7 @@ if
		[[ "$whichStage" == "Counting" ]] \|\|
		[[ "$whichStage" == "Summarising" ]]
		then
		yamlnew=$outdir/$project.postmap.yaml #note! mapping creates a temporary new yaml because of custom GTF!
		if [[ "$isstats" == "yes" ]]; then
		echo "Starting descriptive statistics..."
		if [[ "$isslurm" == "yes" ]]; then

+3 −2

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		@@ -7,7 +7,8 @@ library(methods)
		library(data.table)
		library(yaml)
		library(ggplot2)

		library(Matrix)
		library(dplyr)
		##########################
		myYaml<-commandArgs(trailingOnly = T)
		opt <-read_yaml(myYaml)