Hi,

I have questions with pathview tool. I produced 1 pathway map with log2Foldchange values as input. As a result, I got a map including 9 genes colored red.

I looked into 'pv.out$plot.data.gene' and found that 9 genes had number values in 'all.mapped' column. So does that mean that remaining other genes are not mapped so not colored?

also I thought that 'mol.data' column make use of log2Foldchange. I compared 'mol.data' and log2Foldchange, and found out that for some genes, values are the same and for some other genes, values are not the same.

Example : kegg.names = 2209, labels = FCGR1A, all.mapped = 22092213, mol.data = 10.1918126226888, log2FoldChange = 6.27323853146697

Is this kind of a bug?

Code :

pv.out <- pathview(gene.data = foldchanges, pathway.id = '04145', speices = 'hsa', same.layer = F, limit = c(-10,10))
list.files(pattern = 'hsa04145', full.names = T)
write.csv(pv.out$plot.data.cpd, 'hsa00040_cpd_data.csv')
write.csv(pv.out$plot.data.gene, 'hsa00040_gene_data.csv')
pathview(gene.data = foldchanges, pathway.id = '04145', speices = 'hsa', same.layer = F, limit = c(-10,10))

Please help me. Thank you.