General ⇒ Creating functions in Sweave

[greenStone]

I have a Sweave .Rnw file in R. It does a few things across chunks:

• - Chunk 1: Selects a random integer between 1:4 and saves as variable nPlots.
  
  - Chunk 2: Writes nPlots (random integer selected earlier) number of .txt files to current directory. Writes one .jpg file to current directory.
  
  - Chunk 3: Writes the same .jpg image to the outputted .pdf file generated to the current directory after compilation.

I am trying to figure out how to run these three chunks over and over again. I don't want to copy-and-paste all this code many times, and so I think the best thing for me to do is to create two functions.

The first function would store the new variable nPlots after calling Chunk 1. The second function would be supplied this new variable nPlots, and would call both Chunk 2 and 3.

Then, I could simply have a Chunk 4, where I am calling these two functions several times. Is it possible to accomplish something like this:

Code: Select all

\documentclass{article}
\usepackage{float, hyperref}
\usepackage[margin=1in]{geometry}
\usepackage{graphicx}
\usepackage{hyperref}
\usepackage{caption}

\begin{document}
\SweaveOpts{concordance=TRUE}

\author{myName}
\title{myTitle}

\maketitle

<<options, echo=FALSE>>=
library(knitr)
  opts_chunk$set(cache=TRUE)
@

\section*{mySection}

<<echo=FALSE>>==
library(ggplot2)
library(GGally)
library(stringr)
library(dplyr)
library(matrixStats)
library(gridExtra)
library(reshape2)
@

%%%%%%%% CHUNK 1 %%%%%%%% 

<<echo=FALSE,eval=TRUE>>=
nPlots = sample(1:4, 1)
@

%%%%%%%% CHUNK 2 %%%%%%%% 

<<echo=FALSE,eval=TRUE>>=
set.seed(1)
colList = scales::hue_pal()(nPlots+1)
plotName = "thePlot"

plot_1 <- lapply(1:nPlots, function(i){
  x = data.frame(a=runif(100,0,1),b=runif(100,0,1),c=runif(100,0,1),d=runif(100,0,1))
  x$cluster = "color"
  x$cluster2 = factor(x$cluster)
  xNames = rownames(x)
  write.table(xNames, file = paste(plotName, "_", nPlots, "_", i, ".txt", sep=""), sep=",", row.names=FALSE, col.names=FALSE, quote=FALSE) 
  ggparcoord(x, columns=1:4, groupColumn=6, scale="globalminmax", alphaLines = 0.99) + xlab("Sample") + ylab("log(Count)") + theme(legend.position = "none", axis.title=element_text(size=12), axis.text=element_text(size=12)) + scale_colour_manual(values = c("color" = colList[i]))
})
y = data.frame(a=runif(100,5,6),b=runif(100,5,6),c=runif(100,5,6),d=runif(100,5,6))
y$cluster = "color"
y$cluster2 = factor(y$cluster)
plot_2 = ggparcoord(y, columns=1:4, groupColumn=6, scale="globalminmax", alphaLines = 0.99) + xlab("Sample") + ylab("log(Count)") + theme(legend.position = "none", axis.title=element_text(size=12), axis.text=element_text(size=12)) + scale_colour_manual(values = c("color" = colList[nPlots+1]))

jpeg(file = paste(plotName, "_", nPlots, ".jpg", sep=""))
p = do.call("grid.arrange", c(append(plot_1, list(plot_2)), ncol=1))
invisible(dev.off())
@

%%%%%%%% CHUNK 3 %%%%%%%% 
\begin{figure}[H]
\centering
<<fig=TRUE, echo=FALSE>>=
p = do.call("grid.arrange", c(append(plot_1, list(plot_2)), ncol=1, main=paste(plotName, ": ", nPlots, sep="")))
@
\end{figure}

\end{document}

Thank you for any advice!