Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species

Dear all,
The new SBGNview package has been released with major updates and improvement:
GitHub
github.com/datapplab/SBGNview
BioC
bioconductor.org/packages/SBGNview/

SBGNview is a tool set for pathway based data visualization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview package, with the following key features:
• Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN);
• Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
• Covers 5,200 reference pathways and over 3,000 species by default;
• Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight;
• SBGN pathway data manipulation, processing, extraction and analysis.

You may find an overview and quick start examples here:
github.com/datapplab/SBGNview
Main tutorial:
bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html
Analysis workflow:
bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/pathway.enrichment.analysis.html

Please try it out and let us know if you have any comments/suggestions. Thank you!

I installed the latest release version of SBGNview, and follow the tutorial
bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html
I tried compound data with either one column or two columns (samples). The output color slices are one and two correspondingly. So I was not able to replicate your problem. not sure what happened in your end.
BTW, I would suggest you install the latest version of SBGNview and SBGNview.data. you may need to update your Bioconductor and R too.

My code:

library(SBGNview)
data("sbgn.xmls")
data("pathways.info")
cpd.data <- sim.mol.data(mol.type = "cpd", 
                         id.type = "KEGG COMPOUND accession", 
                         nmol = 10000, 
                         nexp = 2)

SBGNview.obj1 <- SBGNview(cpd.data = cpd.data[,1],
                         input.sbgn = "P00001",
                         output.file = "test_output.cpd.1sample",
                         cpd.id.type = "KEGG",
                         output.formats =  "png")
SBGNview.obj1

SBGNview.obj2 <- SBGNview(cpd.data = cpd.data,
                         input.sbgn = "P00001",
                         output.file = "test_output.cpd.2sample",
                         cpd.id.type = "KEGG",
                         output.formats =  "png")
SBGNview.obj2

one sample output:

two sample output: