Automatic italics into latex tables using xtable in R

xtableCommand.R

library(xtable)
library(plyr)
 
fakedata = data.frame(
 Bacteria = c("G. vaginalis", "L. crispatus"),
 Count = log10(rlnorm(2*100, 13.5))
)

table1 = ddply(fakedata, .(Bacteria), summarize,
  Bacteria = paste("\\textit{",unique(Bacteria),"}", sep=""),
  meanCount = mean(Count)
  )
#the unique statement is a hack to get around a ddply grouping issue 
# \ in front of \textit is an escape character
  
#normal xtable call
print(xtable(table1), include.rownames=FALSE)

#turning off sanitize
print(xtable(table1), include.rownames=FALSE, sanitize.text.function = identity)

#first xtable call output
#> print(xtable(table1), include.rownames=FALSE)
#% latex table generated in R 3.0.1 by xtable 1.7-1 package
#% Tue Dec 31 12:40:34 2013
#\begin{table}[ht]
#\centering
#\begin{tabular}{lr}
#  \hline
#Bacteria & meanCount \\ 
#  \hline
#$\backslash$textit\{G. vaginalis\} & 5.87 \\ 
#  $\backslash$textit\{L. crispatus\} & 5.87 \\ 
#   \hline
#\end{tabular}
#\end{table}

#second xtable call output
#> print(xtable(table1), include.rownames=FALSE, sanitize.text.function = identity)
#\begin{table}[ht]
#\centering
#\begin{tabular}{lr}
#  \hline
#Bacteria & meanCount \\ 
#  \hline
#\textit{G. vaginalis} & 5.87 \\ 
#  \textit{L. crispatus} & 5.87 \\ 
#   \hline
#\end{tabular}
#\end{table}