R: a tool set for pathway based data integration and visualization

# a tool set for pathway based data integration and visualization

## Documentation for package ‘pathview’ version 1.52.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

pathview-package | Pathway based data integration and visualization
bods | Mapping data on KEGG species code and corresponding Bioconductor gene annotation package
col.key | Code molecular data as pseudo colors on the pathway graph
combineKEGGnodes | Special treatment of nodes or edges for KEGG pathway rendering
cpd.accs | Mapping data between compound or gene IDs and KEGG accessions
cpd.names | Mapping data between compound or gene IDs and KEGG accessions
cpd.simtypes | Mapping data between compound or gene IDs and KEGG accessions
cpd2kegg | Mapping between compound IDs and KEGG accessions
cpdidmap | Mapping between compound IDs and KEGG accessions
cpdkegg2name | Mapping between compound IDs and KEGG accessions
cpdname2kegg | Mapping between compound IDs and KEGG accessions
demo.paths | Data for demo purpose
download.kegg | Download KEGG pathway graphs and associated KGML data
eg2id | Mapping between different gene ID and annotation types
gene.idtype.bods | Mapping data between compound or gene IDs and KEGG accessions
gene.idtype.list | Mapping data between compound or gene IDs and KEGG accessions
geneannot.map | Mapping between different gene ID and annotation types
gse16873.d | Data for demo purpose
id2eg | Mapping between different gene ID and annotation types
kegg.met | Mapping data between compound or gene IDs and KEGG accessions
kegg.species.code | Mapping species name to KEGG code
keggview.graph | Pathway based data integration and visualization
keggview.native | Pathway based data integration and visualization
ko.ids | Mapping data between compound or gene IDs and KEGG accessions
korg | Mapping data on KEGG species code and corresponding Bioconductor gene annotation package
mol.sum | Mapping and summation of molecular data onto standard IDs
node.color | Code molecular data as pseudo colors on the pathway graph
node.info | Extract node information from KEGG pathway
node.map | Map molecular data onto KEGG pathway nodes
paths.hsa | Data for demo purpose
pathview | Pathway based data integration and visualization
reaction2edge | Special treatment of nodes or edges for KEGG pathway rendering
rn.list | Mapping data between compound or gene IDs and KEGG accessions
sim.mol.data | Simulate molecular data for pathview experiment
strfit | Wrap or break strings into lines of specified width
wordwrap | Wrap or break strings into lines of specified width