# Using Sweave to include lattice graphics - issues with colour

I am using Sweave and the R package nlme: when including lattice graphics, (encapsulated in the print() command), the .eps files that are generated are all in black and white. The original graphic, (which appears in R) and the saved .pdf file are in colour, but not the .eps.

When including graphics which do not use the lattice package, the .eps files are fine. I have tried including the lattice graphics in one step, e.g.:

\begin{figure}[!h]
\begin{center}
\setkeys{Gin}{width=0.5\textwidth}
<<echo=FALSE,fig=TRUE,width=4,height=4>>=
print(      plot(intervals(sulf1comp.lis),layout=c(3,1,1)#,main="Parameter Estimates     &   95% CI"
))
@
%
\caption{Parameter Estimates and 95\% Confidence Intervals for Individual Model Fits       \label{label sulf_fig2}}
%\label{fig:}
\end{center}
\end{figure}


in two steps, explicitly:

<<figa,echo=FALSE,fig=TRUE,include=FALSE>>=
print(plot(sulf1comp.nls,pid~resid(.,type="p"),abline=0,cex.axis=0.7,
#,main="Plot of Residuals by Subject (Sulfadoxine: NLS Model)"
))
@
%
\begin{figure}[!h]
\begin{center}
\includegraphics*[height=0.5\textwidth]{analysisinprogress_sw-figa.pdf}
\caption{Residuals by Subject ID: Sulfadoxine Bi-Exponential NLS Model \label{label       sulf_fig1}}
\end{center}
\end{figure}
%


Without using the fig=T command, e.g.:

 <<figa,echo=FALSE>>=
postscript("filename.eps")
print(plot(sulf1comp.nls,pid~resid(.,type="p"),abline=0,cex.axis=0.7,
#,main="Plot of Residuals by Subject (Sulfadoxine: NLS Model)"
))
dev.off()
@
%


And various other possibilities. I'm at my wit's end trying to figure out what I'm doing wrong. Any advice would be appreciated.

-

Black and white is the default for eps, whereas color is the default for pdf output.

I'm not sure setting

lattice.options(default.theme = standard.theme(color = TRUE))


would solve your problem, or equivalently (from the Sweave FAQ)

library(lattice)
ltheme <- canonical.theme(color = TRUE)      ## in-built B&W theme
ltheme$strip.background$col <- "transparent" ## change strip bg
lattice.options(default.theme = ltheme)      ## set as default


but do you have any particular reason to prefer Postscript over PDF? I always found that the latter produce very nice looking graphics.

-