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.
I installed the latest release version of SBGNview, and follow the tutorial https://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.