pathview: a tool set for pathway based data integration and visualization
Version 1.16.0

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.

AuthorWeijun Luo
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment Genetics GraphAndNetwork Metabolomics Microarray Pathways Proteomics RNASeq Sequencing SystemsBiology Visualization
Date of publicationNone
MaintainerWeijun Luo <luo_weijun@yahoo.com>
LicenseGPL (>=3.0)
Version1.16.0
URL http://pathview.uncc.edu/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pathview")

Getting started

Package overview

Popular man pages

cpdidmap: Mapping between compound IDs and KEGG accessions
download.kegg: Download KEGG pathway graphs and associated KGML data
eg2id: Mapping between different gene ID and annotation types
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
See all...

All man pages Function index File listing

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

Functions

KEGGEdgeSubtype Man page
KEGGpathway2Graph2 Man page Source code
bods Man page
circles Man page Source code
col.key Man page Source code
colorpanel2 Man page Source code
combineKEGGnodes Man page Source code
cpd.accs Man page
cpd.names Man page
cpd.simtypes Man page
cpd2kegg Man page Source code
cpdidmap Man page Source code
cpdkegg2name Man page Source code
cpdname2kegg Man page Source code
demo.paths Man page
download.kegg Man page Source code
eg2id Man page Source code
ellipses Man page Source code
gene.idtype.bods Man page
gene.idtype.list Man page
geneannot.map Man page Source code
gse16873.d Man page
id2eg Man page Source code
kegg.legend Man page Source code
kegg.met Man page
kegg.species.code Man page Source code
keggview.graph Man page Source code
keggview.native Man page Source code
ko.ids Man page
korg Man page
max.abs Man page Source code
mol.sum Man page Source code
node.color Man page Source code
node.info Man page Source code
node.map Man page Source code
onLoad Source code
parseKGML2 Source code
parseKGML2.R Man page
parseKGML2Graph2 Man page Source code
parseReaction2 Man page Source code
paths.hsa Man page
pathview Man page Source code
pathview-package Man page
pathview.stamp Man page Source code
random Man page Source code
reaction2edge Man page Source code
render.kegg.node Source code
rn.list Man page
sim.mol.data Man page Source code
sliced.shapes Man page Source code
strfit Man page Source code
subtypeDisplay.kedge Man page Source code
wordwrap Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/KEGGpathway2Graph2.R
R/circles.R
R/col.key.R
R/colorpanel2.R
R/combineKEGGnodes.R
R/cpd2kegg.R
R/cpdidmap.R
R/cpdkegg2name.R
R/cpdname2kegg.R
R/download.kegg.R
R/eg2id.R
R/ellipses.R
R/geneannot.map.R
R/id2eg.R
R/kegg.legend.R
R/kegg.species.code.R
R/keggview.graph.R
R/keggview.native.R
R/max.abs.R
R/mol.sum.R
R/node.color.R
R/node.info.R
R/node.map.R
R/parseKGML2.R
R/parseKGML2Graph2.R
R/parseReaction2.R
R/pathview.R
R/pathview.stamp.R
R/random.R
R/reaction2edge.R
R/render.kegg.node.R
R/sim.mol.data.R
R/sliced.shapes.R
R/strfit.R
R/subtypeDisplay.kedge.R
R/wordwrap.R
R/zzz.R
build
build/vignette.rds
data
data/KEGGEdgeSubtype.rda
data/bods.rda
data/cpd.accs.rda
data/cpd.names.rda
data/cpd.simtypes.rda
data/datalist
data/demo.paths.rda
data/gene.idtype.bods.rda
data/gene.idtype.list.rda
data/gse16873.d.rda
data/kegg.met.rda
data/ko.ids.rda
data/korg.rda
data/paths.hsa.rda
data/rn.list.rda
inst
inst/CITATION
inst/doc
inst/doc/pathview.R
inst/doc/pathview.Rnw
inst/doc/pathview.pdf
inst/extdata
inst/extdata/gse16873.demo
inst/extdata/hsa04110.png
inst/extdata/hsa04110.xml
inst/extdata/kegg.sigmet.rda
inst/unitTests
inst/unitTests/test_mapper.R
man
man/combineKEGGnodes.Rd
man/cpd.accs.Rd
man/cpdidmap.Rd
man/demo.data.Rd
man/download.kegg.Rd
man/eg2id.Rd
man/kegg.species.code.Rd
man/korg.Rd
man/mol.sum.Rd
man/node.color.Rd
man/node.info.Rd
man/node.map.Rd
man/pathview-internal.Rd
man/pathview-package.Rd
man/pathview.Rd
man/sim.mol.data.Rd
man/wordwrap.Rd
tests
tests/runTests.R
vignettes
vignettes/pathview.Rnw
vignettes/pathview.bib
pathview documentation built on May 20, 2017, 9:50 p.m.

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