[英]Passing arguments to R script in command line (shell/bash): what to do when column names contain tilde (~)
I'm utilizing Rscript
to run an R script through bash, and I want to specify arguments to be passed to functions within the script itself.我正在利用
Rscript
通过 bash 运行 R 脚本,并且我想指定要传递给脚本本身内函数的参数。 Specifically, I want to pass arguments that specify:具体来说,我想传递指定的参数:
.csv
) and.csv
) 和 I run into a problem when the column names include the tilde sign ( ~
).当列名包含波浪号 (
~
) 时,我遇到了问题。 I've tried wrapping the column names with backticks but still unsuccessful.我试过用反引号包裹列名,但仍然不成功。
I want to write a script that takes in a data file in .csv
format and plots a histogram for one variable according to the user's choice.我想编写一个脚本,它接收
.csv
格式的数据文件,并根据用户的选择为一个变量绘制直方图。
plot_histogram <- function(path_to_input, x_var) {
data_raw <- read.csv(file = path_to_input)
path_to_output_folder <- dirname(path_to_input)
png(filename = paste0(path_to_output_folder, "/", "output_plot.png"))
hist(as.numeric(na.omit(data_raw[[x_var]])), main = "histogram", xlab = "my_var")
replicate(dev.off(), n = 20)
}
set.seed(123)
df <- data.frame(age = sample(20:80, size = 100, replace = TRUE))
write.csv(df, "some_age_data.csv")
plot_histogram(path_to_input = "some_age_data.csv",
x_var = "age")
As intended, I get a .png
file with the plot, saved to the same directory where the .csv
is at正如预期的那样,我得到了一个带有绘图的
.png
文件,保存到.csv
所在的同一目录中
plot_histogram.R
args <- commandArgs(trailingOnly = TRUE)
## same function as above
plot_histogram <- function(path_to_input, x_var) {
data_raw <- read.csv(file = path_to_input)
path_to_output_folder <- dirname(path_to_input)
png(filename = paste0(path_to_output_folder, "/", "output_plot.png"))
hist(as.numeric(na.omit(data_raw[[x_var]])), main = "histogram", xlab = "my_var")
replicate(dev.off(), n = 20)
}
plot_histogram(path_to_input = args[1], x_var = args[2])
Then run via command line using Rscript
然后使用
Rscript
通过命令行运行
$ Rscript --vanilla plot_histogram.R /../../../some_age_data.csv "age"
Works too!也有效!
Step 1: create fake data第 1 步:创建假数据
library(tibble)
set.seed(123)
df <- tibble(`age-blah~value` = sample(20:80, size = 100, replace = T))
write.csv(df, "some_age_data.csv")
Step 2: Using Rscript
:第 2 步:使用
Rscript
:
$ Rscript --vanilla plot_histogram.R /../../../some_age_data.csv "age-blah~value"
Error in hist.default(as.numeric(na.omit(data_raw[[x_var]])), main = "histogram", : invalid number of 'breaks' Calls: plot_histogram -> hist -> hist.default Execution halted
hist.default(as.numeric(na.omit(data_raw[[x_var]])), main = "histogram", : 'breaks' 调用次数无效:plot_histogram -> hist -> hist.default 执行停止
When using Rscript
, how can I pass an argument that specifies a column name containing tilde?使用
Rscript
,如何传递指定包含波浪号的列名的参数? Alternatively, how can I work around .csv
files that have such a format of tilde in column names, within the framework of Rscript
?或者,如何在
Rscript
的框架内处理列名中具有这种波浪号格式的.csv
文件?
Thanks!谢谢!
You are successfully passing an argument that specifies a column name containing tilde.您正在成功传递一个参数,该参数指定包含波浪号的列名。 However,
read.csv
has "fixed" the column names so it doesn't actually contain a tilde.但是,
read.csv
已经“固定”了列名,因此它实际上并不包含波浪号。
read.csv
is silently converting the column name to age.blah.value
. read.csv
正在默默地将列名转换为age.blah.value
。 Use check.names = FALSE
to make it age-blah~value
.使用
check.names = FALSE
使其成为age-blah~value
。
data_raw <- read.csv(file = path_to_input, check.names = FALSE)
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