#' @title Plotting genes to UMIs relationship.
#' @description This function create a plot in which genes are plotted with respect to total counts UMI for each cell.
#' @param file, a character string indicating the path of the file tab delimited of cells un-normalized expression counts.
#' @param umiXgene, a integer defining how many UMI are required to call a gene as present. default: 3
#' @param sep, separator used in count file, e.g. '\\t', ','
#' @return pdf with the cells counts distributions: genes.umi.pdf
#'
#' @export
#'
#' @examples
#' \dontrun{
#' system("wget http://130.192.119.59/public/testSCumi_mm10.csv.zip")
#' unzip("testSCumi_mm10.csv.zip")
#' genesUmi(file=paste(getwd(),"testSCumi_mm10.csv",sep="/"), umiXgene=3, sep=",")
#' }
genesUmi <- function(file, umiXgene=3, sep){
data.folder=dirname(file)
positions=length(strsplit(basename(file),"\\.")[[1]])
matrixNameC=strsplit(basename(file),"\\.")[[1]]
counts.table=paste(matrixNameC[seq(1,positions-1)],collapse="")
matrixName=counts.table
file.type=strsplit(basename(basename(file)),"\\.")[[1]][positions]
counts.matrix=matrixName
#running time 1
ptm <- proc.time()
#running time 1
setwd(data.folder)
tmp <- read.table(paste(counts.matrix,".",file.type,sep=""), sep=sep, header=T, row.names=1, stringsAsFactors = F)
genes <- list()
for(i in 1:dim(tmp)[2]){
x = rep(0, dim(tmp)[1])
x[which(tmp[,i] >= umiXgene)] <- 1
genes[[i]] <- x
}
genes <- as.data.frame(genes)
genes.sum <- apply(genes,2, sum)
umi.sum <- apply(tmp,2, sum)
pdf("genes.umi.pdf")
plot(log10(umi.sum), genes.sum, xlab="log10 UMI", ylab="# of genes")
dev.off()
#running time 2
ptm <- proc.time() - ptm
dir <- dir(data.folder)
dir <- dir[grep("run.info",dir)]
if(length(dir)>0){
con <- file("run.info", "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("casc geneUmi user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("casc geneUmi system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("casc geneUmi elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("casc user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("casc geneUmi system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("casc geneUmi elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
}
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