Package 'pathview' - Bioconductor

16 node.infoExamplesxml.file=system.file("extdata", "hsa04110.xml", package = "pathview")node.data=node.info(xml.file)names(node.data)data(gse16873.d)plot.data.gene=node.map(mol.data=gse16873.d[,1], node.data,node.types="gene")head(plot.data.gene)cols.ts.gene=node.color(plot.data.gene, limit=1, bins=10)head(cols.ts.gene)node.infoExtract node information from KEGG pathwayDescriptionThe parser function, parser KGML file and/or extract node information from KEGG pathway.Usagenode.info(object, short.name = TRUE)Argumentsobjectshort.nameeither a character specifying the full KGML file name (with directory), or aobject of "KEGGPathway" class, or a object of "graphNEL" class. The lattertwo are parsed results of KGML file.logical, if TRUE, the short labels, i.e. the first iterm separated by "," in the longlabels are parsed out as node labels. Default short.name=TRUE.DetailsParser function node.info extract node data from parsed KEGG pathways. KGML files are parsedusing parseKGML2 and KEGGpathway2Graph2. These functions from KEGGgraph package havebeen heavily modified for reaction parsing and conversion to edges.Valuea 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 parsedKEGG pathway.Author(s)Weijun Luo