Hello, I've generated KEGG pathway plot with R package pathview. The code is:
pathview(gene.data = pathwayFC2, pathway.id = keggID2, species = keggID2, kegg.dir = outputDir, kegg.native = FALSE, node.sum = "mean", limit = list("gene"=c(-4, 4)))
kegg.native=FALSE so the plot is generated by graphviz engine. The problem is the color of the node seems differ to my DEGs data parsed.
Below is plot of "Rap1 signaling pathway ". Gene RAP1A has 2 nodes but why with different colors? Gene CDH1 and RAC2 is upgrade their Log2FC are 1.37 and 2.36, but here CDH1 with no color and RAC2 is green. Anyone knows why? Thanks.