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

[Wolfgang Huber]

Ciao Ugo

the function plotPCA is trivial so it is not difficult to replace it with one adapted to your tastes. (Just type ‘plotPCA’ without the ‘()’ in the R command line.) Furthermore, as Mike mentioned, plotPCA returns the trellis object, and you can update it - see e.g. http://stackoverflow.com/questions/6606902/add-labels-on-lattice-xyplot   A working example is:

library("DESeq2")
library("lattice")
example(plotPCA)

myplot = plotPCA(vsd)
names = colData(vsd)$sample

myplot = update(myplot, panel = function(x, y, ...) {
               panel.xyplot(x, y, ...);
               ltext(x=x, y=y, labels=names, pos=1, offset=1, cex=0.8)
            })

There are various packages on CRAN to provide automated moving around of the labels to avoid overplotting, and there are also options for producing the plot as SVG/HTML5 with interactive tooltips …. But then these things are general R and not specific to DESeq2, of course.

best wishes
	Wolfgang


On 10 Feb 2014, at 14:55, Ugo Borello <ugo.borello at inserm.fr> wrote:

> 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]]
>> 
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