Entering edit mode
When using pathview to save the following Sus scrofa KEGG pathway same.layer = TRUE
argument seems to be ignored when also using kegg.native = FALSE
. This is not happening with all the KEGG pathways, however I can't a find a repeat behavior.
Pathway PDF is generated in two sheets with legend on second page. You can check PDF result here: https://www.dropbox.com/s/4o97z1b8ji7diuh/ssc05166.pathview.pdf?dl=0
> genes
100158242 100152267 396960 397628 100738612 100127464 396875 100048932 <NA> 100520726 100624161 767625 100152590 100153002 100141423 397087 100521665 100523914
-3.253765 -3.253765 12.723644 -2.054660 -2.294707 -2.294707 -2.280152 -2.017907 7.720049 -4.358978 -2.883958 -5.870893 2.869302 -2.442875 3.030740 -3.383227 2.012139 -2.406322
pathview(gene.data = genes, pathway.id = "ssc05166", species = "ssc", kegg.native = FALSE, same.layer = TRUE, limit = list(10, cpd=1))
Did mistake when writing the original post, but edited later. Could you please the code (edited in question) and report if you're also getting two pages instead of one?