[BioC] pathview - plotting multiple samples in the same graph?

[Luo Weijun]

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