Pathview produces 3 output files with the following command :
pathview(gene.data = foldchanges, pathway.id = '00040', speices = 'hsa', same.layer = F)
hsa00040.pathview.png (this plot have red or green colors (representing foldchanges))
hsa00040.png (some are colored in green)
hsa00040.xml (I have no idea)
Could you please tell me the difference between these files? What are green colors meaning in hsa00040.png?