pathviewPVT.R

library(pathview)
library(stringr)

dopathview <- function(csvfilepath, pathwayid) {
  df <- read.csv(csvfilepath)
  keggdf <- df[!is.na(df$kegg), ]
  cpdlist <- str_split(keggdf$kegg, "\\|")
  
  log2list <- c()
  for (i in 1:length(cpdlist)) {
    log2list <- c(log2list, setNames(rep(keggdf$log2FC[i], length(cpdlist[[i]])), toupper(cpdlist[[i]])))
  }
  
  pv.out <- pathview(cpd.data = log2list, pathway.id = pathwayid, species = "ath", out.suffix = "atmet.cpd", kegg.native = T)
  
}