pathview (version 1.12.0)

node.info: Extract node information from KEGG pathway

Description

The parser function, parser KGML file and/or extract node information from KEGG pathway.

Usage

node.info(object, short.name = TRUE)

Arguments

object

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.

short.name

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.

Value

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.

Details

Parser function node.info extract node data from parsed KEGG pathways. KGML files are parsed using parseKGML2 and KEGGpathway2Graph2. These functions from KEGGgraph package have been heavily modified for reaction parsing and conversion to edges.

References

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

See Also

pathview the main function, combineKEGGnodes and reaction2edge for special treatment of nodes or edges.

Examples

xml.file=system.file("extdata", "hsa04110.xml", package = "pathview")
node.data=node.info(xml.file)
names(node.data)
#or parse into a graph object, then extract node info
gR1=pathview:::parseKGML2Graph2(xml.file, genesOnly=FALSE, expand=FALSE, split.group=FALSE)
node.data=node.info(gR1)