I have an .Rnw file, containing R code chunks and LaTeX commands. So far, I have been developing and testing this code in Rstudio: clicking on "compile PDF" to obtain some output files and a PDF file generated.
I would now like to use commandArgs() to be able to give my .Rnw one single argument: a YAML file. This file contains all sorts of parameters that are needed by the script.
To give some context:
My .Rnw script is a pipeline script which was designed to be as "generic" as possible.
My .Rnw script requires a number of parameters each time - these will be the parameters varying between each project. To supply these parameters, I currently (already) use a YAML configuration file. This means the first thing my .Rnw script does is import the YAML file, and then it starts doing things.
My problem is: can I used "Rscript", "commandArgs()" and knitr all together. I was hoping that my addind some commandArgs() to my .Rnw script, I would be able to run everything (i.e. give argument on command line to supply YAML file and compile PDF) like so:
Rscript script.Rnw params.yaml
However, I have getting this error about a "\", which I strongly suspect is something to do with the fact I'm using a .Rnw file (and the very first thing in it a LaTeX command). I then saw potential solution on other posts such as:
Rscript -e "library(knitr); knit('script.Rnw')"
pdflatex script.tex
However, this also fails - unsurprisingly I suppose because I haven't given it my configuration YAML file.
I realise my design is likely flawed: by using commandAgrs() AND knitr together, I am making things quite complicated. I also realise that knitr may have not be truly designed for making reports for scripts that are used as pipelines (at least that's my impression). The reason I want to use it is so that for each project, a quick PDF can be generated with all the results.
I would appreciate any advice. Here is a sample of my code:
\documentclass[12pt, a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{hyperref}
\hypersetup{
colorlinks = true, %Colours links instead of ugly boxes
urlcolor = blue, %Colour for external hyperlinks
linkcolor = blue, %Colour of internal links
citecolor = blue %Colour of citations
}
\usepackage{caption}
\setlength{\parindent}{0pt}
\usepackage{authblk}
\usepackage[nomarkers, nolists]{endfloat} %Positions figures at the end of the document and add no list of names (requires that chunk have fig.cap option)
\usepackage{soul} % Allows underline lines to be broken (use \ul{} instead of \underline{})
\usepackage{helvet} %Set up Arial as font
\renewcommand{\familydefault}{\sfdefault}
\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}
\title{\textbf{Report}}
\author{Author}
\date{\today}
\begin{document}
\maketitle
\begingroup
\hypersetup{linkcolor=black} % force independent link colours in table of contents
\tableofcontents
\endgroup
\begingroup
\hypersetup{linkcolor=black} % force independent link colours in list of figures
\listoffigures
\endgroup
\newpage
\section{Introduction}
This report blah blah blah
\newpage
\section{Results}
<<importing-lib, echo=FALSE, message=FALSE, cache=TRUE>>=
###################################################
# Obtain command-line YAML file and set directory #
###################################################
#!/usr/bin/env Rscript
args= commandArgs(trailingOnly=TRUE)
if (length(args) == 0) {
stop("this script requires a configuration file (.yaml) as input")
} else if (length(args) > 1) {
stop("this script requires only one input: a configuration file (.yaml)")
}
params <- yaml.load_file(args[1])
setwd(params$workdir)
if (dir.exists(file.path(params$workdir, "results")) == FALSE) {
dir.create(file.path(params$workdir, "results","edgeR"), recursive = TRUE)
dir.create(file.path(params$workdir, "results", "gsea", "input_files"), recursive = TRUE)
}
print("Hello!")
@
\end{document}
importing-libchunk and put it in its own .R file, add theknitrcommands to that file, and invoke it withRscript. – Alexis