Thank you very much. It will experiment with the code right away. Ugo > From: Wolfgang Huber <whuber at="" embl.de=""> > Date: Mon, 10 Feb 2014 16:27:24 +0100 > To: Ugo Borello <ugo.borello at="" inserm.fr=""> > Cc: Michael Love <michaelisaiahlove at="" gmail.com="">, "Fabrice Chatonnet [guest]" > <guest at="" bioconductor.org="">, <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 > > 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.tr ellis.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 >> >> _______________________________________________ >> 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 >