Hi Everyone

Does anyone know how can I fix the genedata function arguments to plot heatmap for my pathways? is not the rownames of keggres and foldchanges is what is needed? And how can i make the ref =control and samples = tumors ?

pdf("pathwayheatmap.pdf")
head(rownames(keggres) )
for (gs in rownames(keggres$greater) ){
outname = gsub(" |:|/", "_", substr(gs, 10, 100))
geneData(genes = kegg.gs[[gs]], exprs =keggres$greater,
heatmap= T, Colv = F, Rowv = F, dendrogram = "none",  scatterplot = T)
}
dev.off()

But the code all is below:

res$entrez <- mapIds(org.Hs.eg.db,
                     keys=row.names(res),
                     column="ENTREZID",
                     keytype="ALIAS",
                     multiVals="first")


foldchanges = res$logFC
names(foldchanges) = res$entrez
#========================================
#---------- Use Kegg and gage to get upregulated and downregulated pathways
#========================================

datakegg.gs)
keggres = gage(foldchanges, gsets =kegg.gs, same.dir =TRUE, compare="unpaired")
lapply(keggres, head)
write.csv(keggres,"keggres.csv")
keggrespathwaysup = data.frame(id=rownames(keggres$greater), keggres$greater) %>%
  tbl_df() %>%
  filter(row_number()<=5) %>%
  .$id %>%
  as.character()
keggrespathwaysdn = data.frame(id=rownames(keggres$less), keggres$less) %>%
  tbl_df() %>%
  filter(row_number()<=5) %>%
  .$id %>%
  as.character()

#---------------------- 
keggresidsup = substr(keggrespathwaysup, start=1, stop=8)
keggresidsup
keggresidsdn = substr(keggrespathwaysdn, start=1, stop=8)

gobpres = gage(foldchanges, gsets=kegg.gs, same.dir =TRUE, compare ="unpaired")

lapply(gobpres, head)
#========================================
#----------------- Define plotting function for applying later
#========================================

plot_pathway = function(pid) pathview(gene.data=foldchanges,gene.idtype="ENTREZID", pathway.id=pid, species="hsa", new.signature=FALSE)
#---------------- plot multiple pathways ups and downs
tmpup = sapply(keggresidsup, function(pid) pathview(gene.data=foldchanges,gene.idtype="ENTREZID", pathway.id=pid, species="hsa"))
tmpdn = sapply(keggresidsdn, function(pid) pathview(gene.data=foldchanges,gene.idtype="ENTREZID", pathway.id=pid, species="hsa"))

#========================================
#--------------PATHWAY HEATMAP STARTS HERE
#========================================
pdf("pathwayheatmap.pdf")
head(rownames(keggres) )
for (gs in rownames(keggres$greater) ){
outname = gsub(" |:|/", "_", substr(gs, 10, 100))
geneData(genes = kegg.gs[[gs]], exprs = keggres$greater,
heatmap= T, Colv = F, Rowv = F, dendrogram = "none",  scatterplot = T)
}
dev.off()