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

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Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Author
Weijun Luo
Date of publication
None
Maintainer
Weijun Luo <luo_weijun@yahoo.com>
License
GPL (>=3.0)
Version
1.14.0
URLs

View on Bioconductor

Man pages

combineKEGGnodes
Special treatment of nodes or edges for KEGG pathway...
cpd.accs
Mapping data between compound or gene IDs and KEGG accessions
cpdidmap
Mapping between compound IDs and KEGG accessions
demo.data
Data for demo purpose
download.kegg
Download KEGG pathway graphs and associated KGML data
eg2id
Mapping between different gene ID and annotation types
kegg.species.code
Mapping species name to KEGG code
korg
Mapping data on KEGG species code and corresponding...
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
pathview
Pathway based data integration and visualization
pathview-internal
Internal functions
pathview-package
Pathway based data integration and visualization
sim.mol.data
Simulate molecular data for pathview experiment
wordwrap
Wrap or break strings into lines of specified width

Files in this package

pathview/DESCRIPTION
pathview/NAMESPACE
pathview/NEWS
pathview/R
pathview/R/KEGGpathway2Graph2.R
pathview/R/circles.R
pathview/R/col.key.R
pathview/R/colorpanel2.R
pathview/R/combineKEGGnodes.R
pathview/R/cpd2kegg.R
pathview/R/cpdidmap.R
pathview/R/cpdkegg2name.R
pathview/R/cpdname2kegg.R
pathview/R/download.kegg.R
pathview/R/eg2id.R
pathview/R/ellipses.R
pathview/R/geneannot.map.R
pathview/R/id2eg.R
pathview/R/kegg.legend.R
pathview/R/kegg.species.code.R
pathview/R/keggview.graph.R
pathview/R/keggview.native.R
pathview/R/max.abs.R
pathview/R/mol.sum.R
pathview/R/node.color.R
pathview/R/node.info.R
pathview/R/node.map.R
pathview/R/parseKGML2.R
pathview/R/parseKGML2Graph2.R
pathview/R/parseReaction2.R
pathview/R/pathview.R
pathview/R/pathview.stamp.R
pathview/R/random.R
pathview/R/reaction2edge.R
pathview/R/render.kegg.node.R
pathview/R/sim.mol.data.R
pathview/R/sliced.shapes.R
pathview/R/strfit.R
pathview/R/subtypeDisplay.kedge.R
pathview/R/wordwrap.R
pathview/R/zzz.R
pathview/build
pathview/build/vignette.rds
pathview/data
pathview/data/KEGGEdgeSubtype.rda
pathview/data/bods.rda
pathview/data/cpd.accs.rda
pathview/data/cpd.names.rda
pathview/data/cpd.simtypes.rda
pathview/data/datalist
pathview/data/demo.paths.rda
pathview/data/gene.idtype.bods.rda
pathview/data/gene.idtype.list.rda
pathview/data/gse16873.d.rda
pathview/data/kegg.met.rda
pathview/data/ko.ids.rda
pathview/data/korg.rda
pathview/data/paths.hsa.rda
pathview/data/rn.list.rda
pathview/inst
pathview/inst/CITATION
pathview/inst/doc
pathview/inst/doc/pathview.R
pathview/inst/doc/pathview.Rnw
pathview/inst/doc/pathview.pdf
pathview/inst/extdata
pathview/inst/extdata/gse16873.demo
pathview/inst/extdata/hsa04110.png
pathview/inst/extdata/hsa04110.xml
pathview/inst/extdata/kegg.sigmet.rda
pathview/inst/unitTests
pathview/inst/unitTests/test_mapper.R
pathview/man
pathview/man/combineKEGGnodes.Rd
pathview/man/cpd.accs.Rd
pathview/man/cpdidmap.Rd
pathview/man/demo.data.Rd
pathview/man/download.kegg.Rd
pathview/man/eg2id.Rd
pathview/man/kegg.species.code.Rd
pathview/man/korg.Rd
pathview/man/mol.sum.Rd
pathview/man/node.color.Rd
pathview/man/node.info.Rd
pathview/man/node.map.Rd
pathview/man/pathview-internal.Rd
pathview/man/pathview-package.Rd
pathview/man/pathview.Rd
pathview/man/sim.mol.data.Rd
pathview/man/wordwrap.Rd
pathview/tests
pathview/tests/runTests.R
pathview/vignettes
pathview/vignettes/pathview.Rnw
pathview/vignettes/pathview.bib