Tool:SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
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:
Please try it out and let us know if you have any comments/suggestions. Thank you!
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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 SBGNview.data. you may need to update your Bioconductor and R too.
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:
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