Question: pathview - plotting multiple samples in the same graph?
5.1 years ago by
Peter Davidsen • 210
Peter Davidsen • 210 wrote:
Dear List, I recently decided to give the pathview package a try as I would like to map multiple samples data on the same pathway (ie a given node/gene in a KEGG pathway can consist of more than one color). After reading the vignette "Pathview: pathway based data integration and visualization" (version Nov9 2013) I decided to try and reproduce the examples from Chapter 7.2 (page 13-14). However, I'm not able to reproduce figure 6 exactly, as the genes associated to each of the 3 samples inside the gse16873.d matrix seems to be plotted to individual pathways (that is, I end up with 3 png files instead of just 1 for propanoate metabolism) once I run the pathview() command. I have tried playing around with the multi.state and same.layer arguments inside the pathview command, but always end up with 3 png files (one for each sample). I have tried do the example on multiple machines, but end up with the same negative result. Has anyone managed to reproduce figure 6 in the vignette? and if so, did you have to tweak the code in the vignette a bit? R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  grid parallel stats graphics grDevices utils datasets methods base other attached packages:  pathview_1.1.4 org.Hs.eg.db_2.9.0 KEGGgraph_1.16.0 graph_1.38.3  XML_3.95-0.2 plotrix_3.5-3 a4Base_1.8.0 a4Core_1.8.0  a4Preproc_1.8.0 glmnet_1.9-5 Matrix_1.1-2 multtest_2.16.0  limma_3.16.8 genefilter_1.42.0 mpm_1.0-22 KernSmooth_2.23-10  MASS_7.3-29 annaffy_1.32.0 KEGG.db_2.9.1 GO.db_2.9.0  RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1  BiocGenerics_0.6.0 BiocInstaller_1.10.4 gplots_2.12.1 gmodels_188.8.131.52 loaded via a namespace (and not attached):  annotate_1.38.0 bitops_1.0-6 caTools_1.16 gdata_2.13.2 gtools_3.2.1 IRanges_1.18.4  lattice_0.20-24 png_0.1-7 Rgraphviz_2.4.1 splines_3.0.1 stats4_3.0.1 survival_2.37-7  tools_3.0.1 xtable_1.7-1 Kind regards, Peter [[alternative HTML version deleted]]
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