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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()
user2209882
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1 Answers1

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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.

Community
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dwcoder
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    You can also use [`#!/usr/bin/env Rscript` as the shebang line](http://stackoverflow.com/questions/2429511/why-do-people-write-usr-bin-env-python-on-the-first-line-of-a-python-script). – Nick Kennedy Jul 03 '15 at 08:42
  • Getting this error./runr.sh Error: unexpected symbol in " cross_correlation – user2209882 Jul 03 '15 at 08:43
  • Getting wrong @ dwcoder - My 'myscript.r' is #!/usr/bin/Rscript cross_correlation – user2209882 Jul 03 '15 at 08:49