The legend is not plotting for the 3d PCA plot in affycoretools(). From the documentation it says the legend boolean defaults to TRUE, but no legend prints even after I explicitly set the legend boolean to TRUE. Any suggestions on getting the legend to print? I have installed and loaded rgl(). Also, the addtext parameter is not working either. It does not add the sample names as I have specified. Here is my command: plotPCA(expset, pcs=c(1,2,3), plot3d=TRUE, addtext=sampleNames(eset), group = eset$GroupNumber, groupnames=levels(treatment.factors), legend=TRUE) -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] rgl_0.92.894 affycoretools_1.30.0 KEGG.db_2.8.0 [4] GO.db_2.8.0 gplots_2.11.0 MASS_7.3-22 [7] KernSmooth_2.23-8 caTools_1.13 bitops_1.0-4.2 [10] gdata_2.12.0 gtools_2.7.0 VennDiagram_1.5.1 [13] hugene10sttranscriptcluster.db_8.0.1 org.Hs.eg.db_2.8.0 BiocInstaller_1.8.3 [16] mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.8.0 RSQLite_0.11.2 [19] DBI_0.2-5 limma_3.14.1 hugene10stv1cdf_2.11.0 [22] AnnotationDbi_1.20.3 affy_1.36.0 Biobase_2.18.0 [25] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 AnnotationForge_1.0.2 biomaRt_2.14.0 [6] Biostrings_2.26.2 Category_2.24.0 gcrma_2.30.0 genefilter_1.40.0 GOstats_2.24.0 [11] graph_1.36.1 GSEABase_1.20.0 IRanges_1.16.4 lattice_0.20-10 parallel_2.15.1 [16] preprocessCore_1.20.0 RBGL_1.34.0 RCurl_1.95-3 splines_2.15.1 stats4_2.15.1 [21] survival_2.36-14 tools_2.15.1 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 > -- Sent via the guest posting facility at bioconductor.org.

On 11/21/2012 10:34 AM, Guest [guest] wrote: > The legend is not plotting for the 3d PCA plot in affycoretools(). From the documentation it says the legend boolean defaults to TRUE, but no legend prints even after I explicitly set the legend boolean to TRUE. > > Any suggestions on getting the legend to print? You can't with a 3d plot. Hypothetically one could use mtext3d to create a legend outside the plotting region, but I haven't done so, because I never use the 3D plots for anything but interactive peering at the data. > > I have installed and loaded rgl(). > > Also, the addtext parameter is not working either. It does not add the sample names as I have specified. Yep, that doesn't work with rgl either. This would be less work to add, as it is just a call to text3d(). But then again, it is easy enough for you to add as well. See below. > > Here is my command: > > plotPCA(expset, pcs=c(1,2,3), plot3d=TRUE, addtext=sampleNames(eset), group = eset$GroupNumber, groupnames=levels(treatment.factors), legend=TRUE) After the above call to plotPCA(), you can pca <- prcomp(t(exprs(expset))) cnst <- 1 text3d(pca$x[,1]+cnst, pca$x[,2]+cnst, pca$x[,3]+cnst, sampleNames(eset)) You may need to play around with the constant to get the text off the boxes, but you see the idea. Best, Jim > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rgl_0.92.894 affycoretools_1.30.0 KEGG.db_2.8.0 > [4] GO.db_2.8.0 gplots_2.11.0 MASS_7.3-22 > [7] KernSmooth_2.23-8 caTools_1.13 bitops_1.0-4.2 > [10] gdata_2.12.0 gtools_2.7.0 VennDiagram_1.5.1 > [13] hugene10sttranscriptcluster.db_8.0.1 org.Hs.eg.db_2.8.0 BiocInstaller_1.8.3 > [16] mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.8.0 RSQLite_0.11.2 > [19] DBI_0.2-5 limma_3.14.1 hugene10stv1cdf_2.11.0 > [22] AnnotationDbi_1.20.3 affy_1.36.0 Biobase_2.18.0 > [25] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 AnnotationForge_1.0.2 biomaRt_2.14.0 > [6] Biostrings_2.26.2 Category_2.24.0 gcrma_2.30.0 genefilter_1.40.0 GOstats_2.24.0 > [11] graph_1.36.1 GSEABase_1.20.0 IRanges_1.16.4 lattice_0.20-10 parallel_2.15.1 > [16] preprocessCore_1.20.0 RBGL_1.34.0 RCurl_1.95-3 splines_2.15.1 stats4_2.15.1 > [21] survival_2.36-14 tools_2.15.1 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099