Hi Peter, You need to update your pathview to the latest release version, which is 1.2.3. It is at: http://bioconductor.org/packages/release/bioc/html/pathview.html The update history: http://bioconductor.org/packages/release/bioc/news/pathview/NEWS This current release version includes all recent update features, like multiple samples/time series in one graph, and handling of all KEGG species.Your version is pathview_1.1.4, which doesn?t really plot multiple samples in the same graph. To ensure smooth installation, I would suggest you update your R/Bioconductor to the latest version too. Of course, you may always download and install pathview_1.2.3 manually from the link above. HTH, Weijun -------------------------------------------- On Thu, 2/27/14, Peter Davidsen <pkdavidsen at="" gmail.com=""> wrote: Subject: pathview - plotting multiple samples in the same graph? To: bioconductor at r-project.org, bioconductor at stat.math.ethz.ch Date: Thursday, February 27, 2014, 9:44 AM 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: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid ? ? ?parallel ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base ? ? other attached packages: ?[1] pathview_1.1.4 ? ? ? org.Hs.eg.db_2.9.0 ? KEGGgraph_1.16.0 ? ? graph_1.38.3 ? ? ? ? ?[5] XML_3.95-0.2 ? ? ? ? plotrix_3.5-3 ? ? ? ?a4Base_1.8.0 ? ? ? ? a4Core_1.8.0 ? ? ? ? ?[9] a4Preproc_1.8.0 ? ? ?glmnet_1.9-5 ? ? ? ? Matrix_1.1-2 ? ? ? ? multtest_2.16.0 ? ? [13] limma_3.16.8 ? ? ? ? genefilter_1.42.0 ? ?mpm_1.0-22 ? ? ? ? ? KernSmooth_2.23-10 ? [17] MASS_7.3-29 ? ? ? ? ?annaffy_1.32.0 ? ? ? KEGG.db_2.9.1 ? ? ? ?GO.db_2.9.0 ? ? ? ? [21] RSQLite_0.11.4 ? ? ? DBI_0.2-7 ? ? ? ? ? ?AnnotationDbi_1.22.6 Biobase_2.20.1 ? ? ? [25] BiocGenerics_0.6.0 ? BiocInstaller_1.10.4 gplots_2.12.1 ? ? ? ?gmodels_2.15.4.1 ? ? loaded via a namespace (and not attached): ?[1] annotate_1.38.0 bitops_1.0-6 ? ?caTools_1.16 ? ?gdata_2.13.2 ? ?gtools_3.2.1 ? ?IRanges_1.18.4 ?[7] lattice_0.20-24 png_0.1-7 ? ? ? Rgraphviz_2.4.1 splines_3.0.1 ? stats4_3.0.1 ? ?survival_2.37-7 [13] tools_3.0.1 ? ? xtable_1.7-1 Kind regards, Peter

Hi Peter, You need to update your pathview to the latest release version, which is 1.2.3. It is at: http://bioconductor.org/packages/release/bioc/html/pathview.html The update history: http://bioconductor.org/packages/release/bioc/news/pathview/NEWS This current release version includes all recent update features, like multiple samples/time series in one graph, and handling of all KEGG species.Your version is pathview_1.1.4, which doesn?t really plot multiple samples in the same graph. To ensure smooth installation, I would suggest you update your R/Bioconductor to the latest version too. Of course, you may always download and install pathview_1.2.3 manually from the link above. HTH, Weijun -------------------------------------------- On Thu, 2/27/14, Peter Davidsen <pkdavidsen at="" gmail.com=""> wrote: Subject: pathview - plotting multiple samples in the same graph? To: bioconductor at r-project.org, bioconductor at stat.math.ethz.ch Date: Thursday, February 27, 2014, 9:44 AM 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: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid ? ? ?parallel ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base ? ? other attached packages: ?[1] pathview_1.1.4 ? ? ? org.Hs.eg.db_2.9.0 ? KEGGgraph_1.16.0 ? ? graph_1.38.3 ? ? ? ? ?[5] XML_3.95-0.2 ? ? ? ? plotrix_3.5-3 ? ? ? ?a4Base_1.8.0 ? ? ? ? a4Core_1.8.0 ? ? ? ? ?[9] a4Preproc_1.8.0 ? ? ?glmnet_1.9-5 ? ? ? ? Matrix_1.1-2 ? ? ? ? multtest_2.16.0 ? ? [13] limma_3.16.8 ? ? ? ? genefilter_1.42.0 ? ?mpm_1.0-22 ? ? ? ? ? KernSmooth_2.23-10 ? [17] MASS_7.3-29 ? ? ? ? ?annaffy_1.32.0 ? ? ? KEGG.db_2.9.1 ? ? ? ?GO.db_2.9.0 ? ? ? ? [21] RSQLite_0.11.4 ? ? ? DBI_0.2-7 ? ? ? ? ? ?AnnotationDbi_1.22.6 Biobase_2.20.1 ? ? ? [25] BiocGenerics_0.6.0 ? BiocInstaller_1.10.4 gplots_2.12.1 ? ? ? ?gmodels_2.15.4.1 ? ? loaded via a namespace (and not attached): ?[1] annotate_1.38.0 bitops_1.0-6 ? ?caTools_1.16 ? ?gdata_2.13.2 ? ?gtools_3.2.1 ? ?IRanges_1.18.4 ?[7] lattice_0.20-24 png_0.1-7 ? ? ? Rgraphviz_2.4.1 splines_3.0.1 ? stats4_3.0.1 ? ?survival_2.37-7 [13] tools_3.0.1 ? ? xtable_1.7-1 Kind regards, Peter