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

[Ugo Borello]

Dear Mike, 
Regarding the plotPCA() of DESeq2, is there a way to add the sample names on
the plot? 
If not do you plan to modify the function, in the next DESeq2 release, in
order to see the sample names in the plot?

Thank you

Ugo


> From: Michael Love <michaelisaiahlove at gmail.com>
> Date: Mon, 10 Feb 2014 08:42:12 -0500
> To: "Fabrice Chatonnet [guest]" <guest at bioconductor.org>
> Cc: <fabrice.chatonnet at ens-lyon.org>, "bioconductor at r-project.org"
> <bioconductor at r-project.org>
> Subject: Re: [BioC] Problem with exporting graph from plotPCA() in a DESeq2
> function
> 
> 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 at 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 at gmail.com>"
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
> 
> [[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor