[R] legend disappeared after pdf() export to file

[Thierry Janssens]

Dear R-help,

I am trying to print a graph with an additional legend to a pdf() or 
jpeg() file. Unfortunately the legend has completely disappeared in the 
file (pdf of jpeg) compared to what is in the graphics device of the Rgui.
I positioned the legend after retrieving the x,y coordinates by the 
locator() function. No adaptations to  par() have been done.

The chunk of script is as follows (simplified for your convenience)

....
pdf("heatmappearson.pdf")
heatmap.2(cbind(tableTotalforCdheatmap$logFC[sig], 
tableTotalforHeatheatmap$logFC[sig]), labRow = 
tableTotalforCdheatmap$GeneName[sig], labCol = c("Cd", "Heat"), cexRow = 
0.1 , cexCol = 0.9, col = rbg, key = TRUE, keysize = 1, density.info = 
"none", trace = "none", symkey = FALSE, Rowv = TRUE, Colv = FALSE, 
dendrogram = "row",  hclustfun = pearsonfun, RowSideColors = rowcol[sig])
legend(x= 0.84, y = 2.5, legend=legend, fill = c("green", "yellow", 
"orange"))
dev.off()


 > sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United 
Kingdom.1252;LC_MONETARY=English_United 
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
[1] gplots_2.7.0   caTools_1.9    bitops_1.0-4.1 gdata_2.4.2    
gtools_2.5.0-1
[6] statmod_1.3.8  marray_1.20.0  limma_2.16.4 

loaded via a namespace (and not attached):
[1] tools_2.8.1

Any help is welcome.

kind regards,

Thierry Janssens



-- 
Thierry K.S. Janssens
Vrije Universiteit Amsterdam
Faculty of Earth and Life Sciences
Institute of Ecological Science
Department of Animal Ecology,
De Boelelaan 1085
1081 HV AMSTERDAM, The Netherlands
Phone: +31 (0)20-5989147
Fax: +31 (0)20-5987123
thierry.janssens at ecology.falw.vu.nl