I have the commands below that I use to make plots in R. The main text file is cross_correlation.csv.
How can I put it in bash script so that when I launch it on the terminal, the R commands will perform their jobs and finish (like all other shell scripts).
cross_correlation <- read.table(file.choose(), header=F, sep="\t")
barplot(cross_correlation$V3)
dev.copy(png,"cc.png",width=8,height=6,units="in",res=100)
dev.off()
hist(cross_correlation$V3, breaks=15, prob=T)
dev.copy(png,"hist_cc.png",width=8,height=6,units="in",res=100)
dev.off()
If you have R installed, you should also have the program Rscript installed, which can be used to run R scripts:
Rscript myscript.r
So you can put this line in a bash script:
#!/bin/bash
Rscript myscript1.r
Rscript myscript2.r
# other bash commands
This is usually the easiest way to run R scripts inside bash scripts.
If you want to make the script executable so you can run it by typing ./myscript.r, you need to find out where your Rscript is installed by typing:
which Rscript
# /usr/bin/Rscript
Then your myscript.r will look like this
#!/usr/bin/Rscript
cross_correlation <- read.table(file.choose(), header=F, sep="\t")
barplot(cross_correlation$V3)
dev.copy(png,"cc.png",width=8,height=6,units="in",res=100)
dev.off()
hist(cross_correlation$V3, breaks=15, prob=T)
dev.copy(png,"hist_cc.png",width=8,height=6,units="in",res=100)
dev.off()
This method is explained in this question, which might also give you some ideas.
