pathviewCpd.R

library(pathview)
library(stringr)
library(KEGGREST)

foo <- read.csv("foo.csv")
keggdf <- foo[!is.na(foo$kegg),]
cpdlist <- str_split(keggdf$kegg, "\\|")

log2list <- c()
for (i in 1:length(cpdlist)) {
  log2list <- c(log2list, setNames(rep(keggdf$log2FC[i], length(cpdlist[[i]])), toupper(cpdlist[[i]])))
}

pathwayIDfor <- keggLink("pathway", log2list)

# find the most mapped pathwayID
hitslist <- c()
for (i in unique(pathwayIDfor)) {
  hits <- match(i, pathwayIDfor)
}

sim.cpd.data=sim.mol.data(mol.type="cpd", nmol=3000)
pv.out <- pathview(cpd.data = sim.cpd.data, pathway.id = "00020", species = "hsa", out.suffix = "sim.cpd", kegg.native = T)