Running R commands using a bash script

Question

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()

I was about to suggest R CMD BATCH script.r, so in my opinion it's a dupe. — RHertel
– RHertel, Commented Jul 3, 2015 at 8:05
Something like an equivalent to python -c '<commands>' would be nice without having to create a script first. — Soerendip
– Soerendip, Commented Sep 3, 2021 at 16:59

Community · Accepted Answer · 2017-05-23 10:28:05Z

11

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.

edited May 23, 2017 at 10:28

CommunityBot

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answered Jul 3, 2015 at 8:08

dwcoder

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3 Comments

Nick Kennedy Over a year ago

You can also use #!/usr/bin/env Rscript as the shebang line.

user2209882 Over a year ago

Getting this error./runr.sh Error: unexpected symbol in " cross_correlation <- read.table(file.choose(), header=F, sep="\t") cross_correlation.csv" Execution halted ./runr.sh: line 12: syntax error near unexpected token (' ./runr.sh: line 12: cross_correlation <- read.table(file.choose(), header=F, sep="\t")'

user2209882 Over a year ago

Getting wrong @ dwcoder - My 'myscript.r' is #!/usr/bin/Rscript cross_correlation <- read.table(file.choose(), header=F, sep="\t") cross_correlation.csv 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()

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