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

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