[R] 如何在Linux命令行进行参数传入?

之前因为R命令行传参不友好,常常嵌套在其余程序语言(如Perl/Python)中来进行传参,但如今也陆续有一些方式来实现R的传参了,这里简单罗列下。html

方法一

最传统的方法就是使用系统自带的commandArgs函数,直接按位置顺序传入。这种方法简短、快速,适合我的使用。通常也能知足咱们的需求了,但对于其余用户是不够友好的。git

#test.R
args=commandArgs(T)
file=read.table(args[1])
...
#command line
$Rscript test.R file

方法二

使用getopt包,参数形式为:github

getopt(
  spec = NULL, 
  opt = commandArgs(TRUE),
  command = get_Rscript_filename(), 
  usage = FALSE,
  debug = FALSE
)

说明: spec是一个4-5列的矩阵,里面包括了参数信息,前四列是必须的,第五列可选。express

  • 第一列:参数的longname,多个字符。
  • 第二列:参数的shortname,一个字符。
  • 第三列:参数是必须的,仍是可选的,数字:0表明不接参数 ;1表明必须有参数;2表明参数可选。
  • 第四列:参数的类型。logical;integer;double;complex;character;numeric
  • 第五列:注释信息,可选。

应用示例:函数

library(getopt)
# 构建参数矩阵
library(getopt)
spec = matrix(c(
    'verbose', 'v', 2, "integer",
    'help'   , 'h', 0, "logical",
    'count'  , 'c', 1, "integer",
    'mean'   , 'm', 1, "double",), byrow=TRUE, ncol=4)
#传参
opt = getopt(spec)

以个人数据做为例子,部分脚本以下:url

library(getopt)
command=matrix(c("exp","e",1,"character",
                 "ko","k",1,"character",
                 "cazy","z",1,"character",
                 "cog","c",1,"character",
                 "help","h",0,"logical"),byrow=T,ncol=4)
args=getopt(command)
#帮助信息
if (!is.null(args$help) || is.null(args$exp) || is.null(args$ko) || is.null(args$cazy)|| is.null(args$cog)) {
  cat(paste(getopt(command, usage = T), "\n"))
  q()
}

#读入参数
exp <- readr::read_delim(args$exp,delim = "\t")
ko <- readr::read_delim(args$ko,delim = "\t",comment = '#',col_names=F)
cazy <- readr::read_delim(args$cazy,delim = '\t')
cog <- readr::read_delim(args$cog,delim = '\t')
......

命令行运行: 帮助spa

$Rscript getopt_test.R -h
Usage: getopt_test.R [-[-exp|e] <character>] [-[-ko|k] <character>] [-[-cazy|z] <character>] [-[-cog|c] <character>] [-[-help|h]]

运行.net

$ Rscript getopt_test.R --exp protein.xls --ko test.ko --cazy cazy.anno --cog protein2cog.xls

##方法三 使用GetoptLong包。这是由大佬Zuguang Gu开发(就是开发ComplexHeatmapcirclize的那位),借用了Perl GetoptLong模块的传参形式,用法也几乎同样。命令行

GetoptLong(..., help = TRUE, version = TRUE, envir = parent.frame(), argv_str = NULL,
    head = NULL, foot = NULL, script_name = NULL)

能够看下他提供的例子: https://github.com/jokergoo/GetoptLong https://www.rdocumentation.org/packages/GetoptLong/versions/0.1.7/topics/GetoptLongdebug

#r script
library(GetoptLong)
    cutoff = 0.05 #default
    GetoptLong(
        "number=i", "Number of items, integer, mandatory option",
        "cutoff=f", "cutoff to filter results, optional, default (0.05)",
        "verbose",  "print messages"
    )  

#Then you can call the script from command line either by:
    $ Rscript foo.R --number 4 --cutoff 0.01 --verbose
    $Rscript foo.R -n 4 -c 0.01 -v
    $ Rscript foo.R -n 4 --verbose

以我本身的数据为例。部分R脚本以下:

suppressMessages(library(GetoptLong))
suppressMessages(library(tidyverse))

GetoptLong(
  "expression=s", "protein expression matrix",
  "ko=s", "ko annotation outcome",
  "cazy=s", "cazy annotation outcome",
  "cog=s", "cog annotation outcome",
  "verbose!","print messages"
)

#读入参数
exp <- readr::read_delim(expression,delim = "\t")
ko <- readr::read_delim(ko,delim = "\t",comment = '#',col_names=F)
cazy <- readr::read_delim(cazy,delim = '\t')
cog <- readr::read_delim(cog,delim = '\t')

命令行运行会自动生成帮助文档。

$ Rscript test.R --help
Usage: Rscript function_summary.R [options]

  --expression character
    protein expression matrix

  --ko character
    ko annotation outcome

  --cazy character
    cazy annotation outcome

  --cog character
    cog annotation outcome

  --verbose
    print messages

  --help
    Print help message and exit.

  --version
    Print version information and exit.

长参传入:

$Rscript test.R --expression protein.xls --ko test.ko --cazy cazy.anno --cog protein2cog.xls

短参传入: 若是全部参数的首字母不一样,用首字母便可;若是有些参数名称近似,则最好用多个字母,不然会辨别不了。 好比我这里的cogcazy参数,首字母相同,明显不能都用c,我把其中一个改为大写的C也辨别不了;其中一个用一个首字母,另外一个用两个首字母也不行。用coca就能够了。因此参数的名字必定要明显区分开来。

$ Rscript test.R -e protein.xls -k test.ko -c cazy.anno -C protein2cog.xls
Option c is ambiguous (cazy, cog)
Option c is ambiguous (cazy, cog)
Usage: Rscript test.R [options]

  --expression character
    protein expression matrix

  --ko character
    ko annotation outcome

  --cazy character
    cazy annotation outcome

  --Cog character
    cog annotation outcome

  --verbose
    print messages

  --help
    Print help message and exit.

  --version
    Print version information and exit.

这个就能够了

$ Rscript test.R -e protein.xls -k test.ko -ca cazy.anno -co protein2cog.xls

Ref: https://www.cnblogs.com/timeisbiggestboss/p/7811009.html https://www.rdocumentation.org/packages/GetoptLong/versions/0.1.7/topics/GetoptLong

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