Hi,

I wrote some codes. Explanations are below: 

# Loading required packages

library("VariantAnnotation")
library("TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")

# args will take different values (VCF files) while running the script from command line 

args <- commandArgs(trailingOnly = TRUE)

file1<- table(seqnames(readVcf(args[1],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))
file2<- table(seqnames(readVcf(args[2],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))
file3<- table(seqnames(readVcf(args[3],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))
file4<- table(seqnames(readVcf(args[4],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))
file5<- table(seqnames(readVcf(args[5],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))
file6<- table(seqnames(readVcf(args[6],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))

all<- rbind(file1, file2, file3, file4, file5, file6)
all<- as.matrix(all)

pdf("Barplot_of_mutaton.pdf")

barplot(all, beside=TRUE, col= rainbow(nrow(all)),
        legend=rownames(all), cex.names=0.7, args.legend = list(x = "topright",bty = "n",
                                                                inset=c(-0.07, -0.14)))
dev.off()

This script was for 6 inputs. This worked properly. 

Now, I want to make a function, that will take input, while I run the script through command line. Input could be 1 to n. But it should plot the barplot.

For example: if I input 2 files, than also it should plot a barplot and if I provide input of 10 files, than also script should work. I am not good at writing functions, but tried the following commands:

args <- commandArgs(trailingOnly = TRUE)
args<- NULL
for (i in args) {
  library("VariantAnnotation")
  library("TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")
  args[i]<- table(seqnames(readVcf(args[i],"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")))
  all<- rbind(args[i])
  pdf("Barplot_of_mutaton.pdf")
  barplot(all, beside=TRUE, col= rainbow(nrow(all)),
          legend=rownames(all), cex.names=0.7, args.legend = list(x = "topright",bty = "n",
                                                                  inset=c(-0.07, -0.14)))
  dev.off()
}

Regards,

Deepak

I am guessing that the problem you're having is that only the last file appears in your PDF?  Try putting your pdf() before the loop and dev.off() after the loop to get a multi-page PDF file rather than over-writing it with each loop.