## ---- echo = FALSE--------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## -------------------------------------------------------------------------- # if(!"rWikiPathways" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rWikiPathways") # } # library(rWikiPathways) ## -------------------------------------------------------------------------- # listOrganisms() ## -------------------------------------------------------------------------- # hs.pathways <- listPathways('Homo sapiens') # hs.pathways ## -------------------------------------------------------------------------- # ?listPathways # length(hs.pathways) ## -------------------------------------------------------------------------- # ?listPathwayIds # ?listPathwayNames # ?listPathwayUrls ## -------------------------------------------------------------------------- # tnf.pathways <- findPathwaysByXref('TNF','H') # tnf.pathways ## -------------------------------------------------------------------------- # ?findPathwayIdsByXref # ?findPathwayNamesByXref # ?findPathwayUrlsByXref ## -------------------------------------------------------------------------- # getPathwayInfo('WP554') ## -------------------------------------------------------------------------- # getXrefList('WP554','L') ## -------------------------------------------------------------------------- # getXrefList('WP554', 'En') ## -------------------------------------------------------------------------- # getXrefList('WP554', 'Ch') # getXrefList('WP554', 'Ce') # getXrefList('WP554', 'Cs') ## -------------------------------------------------------------------------- # gpml <- getPathway('WP554') ## -------------------------------------------------------------------------- # svg <- getColoredPathway('WP554') ## -------------------------------------------------------------------------- # svg = getColoredPathway(pathway="WP554", graphId="ef1f3", color="DD88FF"); ## -------------------------------------------------------------------------- # downloadPathwayArchive() ## -------------------------------------------------------------------------- # downloadPathwayArchive(organism="Mus musculus", format="gmt") ## -------------------------------------------------------------------------- # downloadPathwayArchive(date="20171010", organism="Mus musculus", format="gmt") ## -------------------------------------------------------------------------- # browseVignettes('rWikiPathways') # help(package='rWikiPathways')