Dear Laurent in pRoloc::plot2D the plot is a side effect (via graphics::plot), and therefore you are free to return something else; while in the function discussed below the plot (a 'trellis' object) is the return value, which then usually is rendered via 'print.trellis'. (One could stick additional information like the PCA loadings and eigenvalues into the same (S3-)object, initially I thought this was ugly but maybe it's the way to go.) Best wishes Wolfgang On Aug 6, 2013, at 9:33 pm, Laurent Gatto <lg390 at="" cam.ac.uk=""> wrote: > On 6 August 2013 16:32, Wolfgang Huber <whuber at="" embl.de=""> wrote: >> @all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value. > > I have a similar function (pRoloc::plot2D) that invisibly returns the > prcomp(...)$x[, dims] matrix that used for plotting, where dims are > the PCs requested by the user (default being 1:2). I also report the > proportion of variance explained by these two components on the axes. > > Best wishes, > > Laurent > >> Best wishes >> Wolfgang >> >> >> >> On 6 Aug 2013, at 08:54, Alexey Moskalev <amoskalev at="" list.ru=""> wrote: >> >>> I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq? >>> [[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 > > > > -- > Laurent Gatto > - http://proteome.sysbiol.cam.ac.uk/lgatto/ > Cambridge Centre for Proteomics > - http://www.bio.cam.ac.uk/proteomics > Using R/Bioconductor for proteomics data analysis > - http://lgatto.github.io/RforProteomics/