/rwikipathways

R client package for the WikiPathways API.

Primary LanguageR

Build Status

R Client Package for WikiPathways

R Client library for the WikiPathways API (https://webservice.wikipathways.org/) (license: MIT).

WikiPathays is described in the NAR paper by Kutmon et al.

If you like this package, or want to make it easier to work with Xrefs, then you may also like these R packages:

How to install

install.packages(c("curl", "plyr", "jsonlite")) # dependencies
install.packages("testthat") # if you want to test the package
install.packages("devtools") # to install from GitHub
library(devtools)
install_github("egonw/rwikipathways", subdir="rWikiPathways")

For RStudio installation

library("curl")
library("plyr")
library("jsonlite")
install.packages("devtools")
library("devtools")

library("RCurl")
library("bitops")
library("urltools")

install_github("egonw/rwikipathways", subdir="rWikiPathways")
library("rWikiPathways")

Examples

organisms = listOrganisms()
pathways = listPathways()
humanPathways = listPathways(organism="Homo sapiens")
gpml = getPathway(pathway="WP4")
gpml = getPathway(pathway="WP4", revision=83654)
info = getPathwayInfo(pathway="WP4")
xrefs = getXrefList(pathway="WP2338", systemCode="S")
pathways = findPathwaysByXref("HMDB00001", "Ch")
pathways = findPathwaysByXref(identifier="HMDB00001", systemCode="Ch")
pathways = findPathwaysByXref(
    identifier=c("HMDB00001", "HMDB00002"),
    systemCode=c("Ch", "Ch")
)
svg = getColoredPathway(pathway="WP1842", graphId=c("dd68a","a2c17"));
svg = getColoredPathway(pathway="WP1842", graphId=c("dd68a","a2c17"),
    color="00FF00");
svg = getColoredPathway(pathway="WP1842", graphId=c("dd68a","a2c17"),
    color=c("FF0000", "00FF00"));
writeLines(svg, "pathway.svg")