[BioC] Problem with exporting graph from plotPCA() in a DESeq2 function

[Fabrice Chatonnet [guest]]

Hi!

I am currently programming a function for easy use of DESeq2. I would like to export my graphs with the pdf() command. It works fine for the dispersion graph and other volcano plots that I programmed, but I encountered some problems with the plotPCA() function. First I have to execute it at the very end of the function to see the graph, and the if I use pdf()... dev.off / graphics.off(), the pdf file contains all graphs but the PCA graph.
I tried it line by line in the console, it works fine.
I usually work with RStudio, but under R it didn't work either. Any ideas?

Thanks for your help,

Fabrice.

 -- output of sessionInfo(): 

> sessionInfo("DESeq2")
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
character(0)

other attached packages:
[1] DESeq2_1.2.10

loaded via a namespace (and not attached):
 [1] annotate_1.40.0         AnnotationDbi_1.24.0    base_3.0.2             
 [4] Biobase_2.22.0          BiocGenerics_0.8.0      BiocInstaller_1.12.0   
 [7] datasets_3.0.2          DBI_0.2-7               genefilter_1.44.0      
[10] GenomicRanges_1.14.4    graphics_3.0.2          grDevices_3.0.2        
[13] grid_3.0.2              IRanges_1.20.6          lattice_0.20-24        
[16] locfit_1.5-9.1          methods_3.0.2           parallel_3.0.2         
[19] RColorBrewer_1.0-5      Rcpp_0.11.0             RcppArmadillo_0.4.000.2
[22] rJava_0.9-6             RSQLite_0.11.4          splines_3.0.2          
[25] stats_3.0.2             stats4_3.0.2            survival_2.37-7        
[28] tools_3.0.2             utils_3.0.2             xlsx_0.5.5             
[31] xlsxjars_0.5.0          XML_3.98-1.1            xtable_1.7-1           
[34] XVector_0.2.0

> packageDescription('DESeq2')$Maintainer
[1] "Michael Love <michaelisaiahlove at gmail.com>"

--
Sent via the guest posting facility at bioconductor.org.