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

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


Dear all,
The new SBGNview package has been released with major updates and improvement:

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:
Main tutorial:
Analysis workflow:

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



pathway analysis




I installed the latest release version of SBGNview, and follow the tutorial
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 you may need to update your Bioconductor and R too.

My code:

data("") <- = "cpd", 
                         id.type = "KEGG COMPOUND accession", 
                         nmol = 10000, 
                         nexp = 2)

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

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

one sample output:
one sample output

two sample output:
two sample output:

before adding your answer.

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