|Colored pathways created with|
the new R package.
Of course, hiding those details is not so much of an issue, and since I have made so many R packages in the past, I decided to pick up the request to create an R package for WikiPathways: rWikiPathways. It is not feature complete yet, and not extensively tested in daily use yet (there is a test suite). But here are some code examples. Listing pathways and organisms in the wiki is done with:
For the technology oriented users, for each pathway, you have access to the GPML source file for each pathway:
organisms = listOrganisms() pathways = listPathways() humanPathways = listPathways(organism="Homo sapiens")
However, most use will likely be via database identifiers for genes, proteins, and metabolites, called Xrefs (also check out the R package for BridgeDb):
gpml = getPathway(pathway="WP4") gpml = getPathway(pathway="WP4", revision=83654)
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")
Of course, these are just the basics, and the question was about colored pathways. The SOAP code was a bit more elaborate, and this is the version with this new package (the result at the top of this post):
If you use this package in your research, please cite the below WikiPathways paper. If you have feature requests, please post the in the issue tracker.
svg = getColoredPathway(pathway="WP1842", graphId=c("dd68a","a2c17"), color=c("FF0000", "00FF00")); writeLines(svg, "pathway.svg")
Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E. L., Bohler, A., Mélius, J., Waagmeester, A., Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T., Pico, A. R., Oct. 2015. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Research. http://dx.doi.org/10.1093/nar/gkv1024