combineKEGGnodes {pathview} | R Documentation

## Special treatment of nodes or edges for KEGG pathway rendering

### Description

`combineKEGGnodes` combines nodes into a group in a KEGG pathway graph. `reaction2edge` converts reactions into edges in KEGG pathway graph.

### Usage

    combineKEGGnodes(nodes, graph, combo.node)
    reaction2edge(path, gR)

### Arguments

`nodes` | character, names of the names to be combined.
`graph, gR` | a object of "graphNEL" class, the graph parsed and converted from KEGG pathway.
`path` | a object of "KEGGPathway" class, the parsed KEGG pathway.
`combo.node` | character, the name of result combined node.

### Details

`combineKEGGnodes` not only combines nodes in the graph object, but also corresponding node data in the KEGG pathway object. This function is needed for KEGG-defined group nodes and parsed enzyme groups involved in the same reaction. `reaction2edge` converts a reaction into 2 consecutive edges between substrate and enzyme and enzyme and product. This function is needed as to faithfully show the compound-enzyme nodes and their interactions in Graphviz-style view of KEGG pathway.

### Value

The results returned by `combineKEGGnodes` is a combined graph of "graphNEL" class. The results returned by `reaction2edge` is a list of 3 elements: `gR`, the converted graph ("graphNEL"); edata.new, the new edge data ("KEGGEdge"); ndata.new, the new node data ("KEGGNode").

### 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

`node.info` the main parser function

[Package pathview version 1.28.1 Index]