I am doing Deseq2 analysis and would like to save all the plots in a single pdf file. For that i have written a function and try to use the function to save plots one after the other in a single pdf file. Here is the sample code and so far i was not succesful
pdf="Results_Deseq2.pdf"
if (!(is.null(pdf))){
pdf(pdf,paper="a4r")
}
window=function(x){
if(is.null(pdf)){
windows()
} else {
par(mfrow=c(1,1))
}
##### Analysis##########
window()
DESeq2::plotMA(dds)
dev.off()
rld <- rlog(dds, blind=FALSE) # rlog
vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
notAllZero <- (rowSums(counts(dds))>0)
par(mfrow=c(2,2))
window()
meanSdPlot(log2(counts(dds,normalized=TRUE) + 1)) ## log transformation log2(n+1) counts
meanSdPlot(assay(rld[notAllZero,])) ##rlog transformation
meanSdPlot(assay(vsd[notAllZero,])) ##variance stabilizing transformation
distro_expr(rld,plot_type = "boxplot")
dev.off()