## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install('biodbKegg') ## ----results='hide'----------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- kegg.comp.conn <- mybiodb$getFactory()$createConn('kegg.compound') ## ----------------------------------------------------------------------------- entries <- kegg.comp.conn$getEntry(c('C00133', 'C00751')) entries ## ----------------------------------------------------------------------------- x <- mybiodb$entriesToDataframe(entries, compute=FALSE) x ## ----------------------------------------------------------------------------- ids <- kegg.comp.conn$searchForEntries(list(monoisotopic.mass=list(value=64, delta=2.0)), max.results=10) entries <- mybiodb$getFactory()$getEntry('kegg.compound', ids) ## ----Data frame with a column containing KEGG Compound IDs-------------------- kegg.comp.ids <- c('C06144', 'C06178', 'C02659') mydf <- data.frame(kegg.ids=kegg.comp.ids) ## ----Calling addInfo()-------------------------------------------------------- kegg.comp.conn$addInfo(mydf, id.col='kegg.ids', org='mmu') ## ----------------------------------------------------------------------------- kegg.comp.ids <- c('C06144', 'C06178', 'C02659') pathways <- kegg.comp.conn$getPathwayIds(kegg.comp.ids, 'mmu') pathways ## ----------------------------------------------------------------------------- path.per.comp <- kegg.comp.conn$getPathwayIdsPerCompound(kegg.comp.ids, 'mmu') fct <- function(i) { if (i %in% names(path.per.comp)) length(path.per.comp[[i]]) else 0 } nb_mmu_gene_pathways <- vapply(kegg.comp.ids, fct, FUN.VALUE=0) names(nb_mmu_gene_pathways) <- kegg.comp.ids ## ----------------------------------------------------------------------------- nb_mmu_gene_pathways ## ----Getting a connector to the KEGG Pathway database------------------------- kegg.path.conn <- mybiodb$getFactory()$getConn('kegg.pathway') ## ----Building a pathway graph------------------------------------------------- kegg.path.conn$buildPathwayGraph(pathways[[1]]) ## ----Getting an igraph for the pathway---------------------------------------- ig <- kegg.path.conn$getPathwayIgraph(pathways[[1]]) ## ----Plotting the pathway igraph---------------------------------------------- vert <- igraph::as_data_frame(ig, 'vertices') shapes <- vapply(vert[['type']], function(x) if (x == 'reaction') 'rectangle' else 'circle', FUN.VALUE='', USE.NAMES=FALSE) colors <- vapply(vert[['type']], function(x) if (x == 'reaction') 'yellow' else 'red', FUN.VALUE='', USE.NAMES=FALSE) plot(ig, vertex.shape=shapes, vertex.color=colors, vertex.label.dist=1, vertex.size=4, vertex.size2=4) ## ----Getting the enzymes------------------------------------------------------ kegg.enz.ids <- mybiodb$entryIdsToSingleFieldValues(kegg.comp.ids, db='kegg.compound', field='kegg.enzyme.id') kegg.enz.ids ## ----Attributing colors to entries-------------------------------------------- color2ids <- list(yellow=kegg.enz.ids, red=kegg.comp.ids) ## ----Creating a decorated pathway picture, message=FALSE---------------------- kegg.path.conn$getDecoratedGraphPicture(pathways[[1]], color2ids=color2ids) ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- sessionInfo()