hi Fabrice,

plotPCA() returns a call to xyplot() which is a function of the lattice
package.  I didn't try this yet, but typically the solution with lattice
plots is a print call:

plt <- plotPCA(...)
print(plt)

see
http://stat.ethz.ch/R-manual/R-devel/library/lattice/html/print.trellis.html

Mike


On Mon, Feb 10, 2014 at 8:32 AM, Fabrice Chatonnet [guest] <
guest@bioconductor.org> wrote:

>
> 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@gmail.com>"
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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