node.info {pathview} | R Documentation

## 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.

### 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.

### 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.

### Author(s)

Weijun Luo <luo_weijun@yahoo.com>

### 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)

[Package pathview version 1.28.1 Index]