generate a PDF containing R output inside latex table

Question

I wrote a script that generates 4 variables from 2 for loops, each one of them contain a big number of data. I want to place these variables inside a data frame and then create a latex table so I can output it as a PDF.

t <- read.table("data.txt", stringsAsFactors=FALSE)
uni <- unique(c(t$V9))

testresult <- function(column, datacol) {    
  if(column=="PP") {
    for (xp in uni) { 
      for(yp in uni) {
        testx <- subset(t, V9==xp)
        testy <- subset(t, V9==yp)
        zz <- wilcox.test(testx[[datacol]],jitter(testy[[datacol]]))
        p.value <- zz$p.value
      }
    }
  } 
}

I want the table to contain these 4 columns (xp, yp, p-value, significance) for each xp and yp in the 2 for loops.

The question about whether the jitter in my function is appropriate has been taken to stats.stackexchange.com: is it wrong to jitter before performing wilcox test

Answer 1

To make a data frame with your results, use rbind to add the results by row to an output object within the loop, as shown with the out object below.

To get a LaTeX table from the data frame, use xtable.

The easiest way to make all this happen is with an Sweave document, like the following. If you don't want to use Sweave, you can just run the R code and copy/paste the resulting LaTeX tables into your own LaTeX document.

\documentclass{article}
\begin{document}
<<echo=FALSE, results=hide>>=
# make up some data
set.seed(5)
N <- 15
t <- data.frame(a=round(runif(N)*100), 
                b=round(runif(N)*100),
                V9=rep(LETTERS[1:3],N/3), 
                stringsAsFactors=FALSE)
uni <-  unique(c(t$V9))

# function to get result for a particular data column
testresult<- function(column, datacol) {    
  out <- NULL
  if(column=="PP") {
    for (xp in uni) { 
      for(yp in uni) {
        testx <- subset(t, V9==xp)
        testy <- subset(t, V9==yp)
        zz <- wilcox.test(testx[[datacol]],jitter(testy[[datacol]]))
        out <- rbind(out, data.frame(xp=xp, yp=yp, p.value=zz$p.value))
      }
    }
  } 
  out
}

# get results for columns a and b
ta <- testresult("PP","a")
tb <- testresult("PP","b")

# load xtable library for output
library(xtable)
@ 

\section*{a results}
<<results=tex, echo=FALSE>>=
print(xtable(ta), include.rownames=FALSE, floating=FALSE)
@ 

\section*{b results}
<<results=tex, echo=FALSE>>=
print(xtable(tb), include.rownames=FALSE, floating=FALSE)
@ 

\end{document}

If you'd rather not Sweave, you could do something like what the latex function of Hmisc does and create the .tex file from within R and then do a system call to pdflatex. Here's a function that would do that on a table tab, outputting the results to a file with basename file.

pdfit <- function(tab, file) {
  texfile <- paste(file, ".tex", sep="")
  cat("\\documentclass{article}\n\\begin{document}\n", file=texfile)
  print(xtable(tab), include.rownames=FALSE, floating=FALSE, 
        file=texfile, append=TRUE)
  cat("\\end{document}\n", file=texfile, append=TRUE)
  sys(paste("pdflatex", texfile))
}
pdfit(ta, "ta")

Answer 2

If you can save the table to a text file, I think you can import it in LaTeX with the pgfplotstable package. From its documentation:

PgfplotsTable is a lightweight sub-package of pgfplots which employs its table input methods and the number formatting techniques to convert tab-separated tables into tabulars.

Its input is a text file containing space separated rows, possibly starting with column names. Its output is a LaTeX tabular which contains selected columns of the text table, rounded to the desired precision, printed in the desired number format (fixed point, integer, scientific etc.).