Pathview and the use of conversion IDs

Question

[l.willianpacheco]

Hi everyone

I am looking for a tutorial or example that use the conversion IDs option in pathview package. My problem: my IDs are converted but the the log2FC are not used for the color on the map.

library(org.Sbicolor.Pythozome12.eg.db)
library(pathview)

DEGs<-read.csv("DEGs/Sorghum-DEGs.txt", header=T, sep="\t")[,1:2]
head(DEGs)
                 log2FC
Sobic.009G014600 -3.98586
Sobic.003G370600 -3.98265
Sobic.010G160033 -3.88334
Sobic.010G026500 -3.61378
Sobic.007G138600 -3.57887
Sobic.001G365100 -3.49684

rownames(DEGs)<-DEGs$gene
DEGs$gene<-NULL

temp<-pathview(gene.data = DEGs, pathway.id = "00010", 
         limit=list(gene=4, cpd=4), gene.annotpkg = "org.Sbicolor.Pythozome12.eg.db",
         species = "sbi", out.suffix = "Glycolysis_Gluconeogenesis")

head(temp)
   kegg.names  labels all.mapped type   x   y width height log2FC mol.col
18    8070439 8070439            gene 483 407    46     17     NA #FFFFFF
42    8078880 8078880            gene 284 948    46     17     NA #FFFFFF
48    8075118 8075118            gene 378 915    46     17     NA #FFFFFF
49    8058902 8058902            gene 487 948    46     17     NA #FFFFFF
50    8056438 8056438            gene 439 941    46     17     NA #FFFFFF

But, yeah! When I convert the IDs to Entrez and use it as input, this works ok. I am implementing this code to a tutorial for the lab, and the convertion would be a easy way to implement this code.

Willian :D