pathview - plotting multiple samples in the same graph?
1
0
Entering edit mode
@peter-davidsen-4584
Last seen 7.2 years ago
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 [[alternative HTML version deleted]]
Pathways GO pathview Pathways GO pathview • 1.3k views
ADD COMMENT
0
Entering edit mode
@peter-davidsen-4584
Last seen 7.2 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140227="" 6bd12ca9="" attachment-0001.pl="">
ADD COMMENT
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode
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
ADD REPLY

Login before adding your answer.

Traffic: 432 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6