The parser function, parser KGML file and/or extract node information from KEGG pathway.
either a character specifying the full KGML file name (with directory), or a object of "KEGGPathway" class, or a object of "graphNEL" class. The latter two are parsed results of KGML file.
logical, if TRUE, the short labels, i.e. the first iterm separated by "," in the long labels are parsed out as node labels. Default short.name=TRUE.
Parser function node.info extract node data from parsed KEGG
pathways. KGML files are parsed using
KEGGpathway2Graph2. These functions from KEGGgraph package have
been heavily modified for reaction parsing and conversion to
a named list of 10 elements: "kegg.names", "type", "component", "size", "labels", "shape", "x", "y", "width" and "height". Each elements record the corresponding attribute for all nodes in the parsed KEGG pathway.
Weijun Luo <[email protected]>
Luo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integration and visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285
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