使用bash脚本运行R命令 [英] Running R commands using a bash script

问题描述

我有以下命令可用于在R中进行绘图。主要文本文件为cross_correlation.csv。

I have the commands below that I use to make plots in R. The main text file is cross_correlation.csv.

如何将其放入bash脚本中，以便在终端上启动它时，R命令将执行其工作并完成操作（就像所有其他shell脚本一样）。

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()

推荐答案

如果安装了R，则还应该安装程序 Rscript ，该程序可用于运行R脚本：

If you have R installed, you should also have the program Rscript installed, which can be used to run R scripts:

Rscript myscript.r

因此您可以将此行放入bash脚本中：

So you can put this line in a bash script:

#!/bin/bash

Rscript myscript1.r
Rscript myscript2.r
# other bash commands

这通常是在bash脚本中运行R脚本的最简单方法。

This is usually the easiest way to run R scripts inside bash scripts.

如果要使脚本可执行，则可以通过键入来运行它./myscript.r ，您需要输入以下内容来找出 Rscript 的安装位置：

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

然后您的 myscript.r 看起来像这样

#!/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()

此方法此问题，可能还会给您一些想法。

This method is explained in this question, which might also give you some ideas.

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