Suspected error in pagoda.show.pathways

[Jens von Preußen]

Hi Jean and Peter,

I suspect an error in the way pagoda.show.pathways orders rows when called with gene names.

Consider a list of genes, that I'm interested in. When plotting the genes with pagoda.show.pathways, the first plot in the attachment is generated.
Now I change the order of the genes in that list (e.g. to have them in order of correlation to another gene not in the list). As you can see in the second plot attached, the main matrix does not change at all, but the "summary" on the left side changes.
Is this behavior intended or correct in any way?

Thanks for a quick reply. In the mean time I try to look into the code and figure out, what it might be.

Best,
Jens

P.S.: The lists I give are indeed differently ordered, as a head() confirms:

$list1:
[1] "ENSMUSG00000032187" "ENSMUSG00000024921" "ENSMUSG00000023018" "ENSMUSG00000078619" "ENSMUSG00000028949"
[6] "ENSMUSG00000031715"
$list2:
[1] "ENSMUSG00000028949" "ENSMUSG00000041229" "ENSMUSG00000020390" "ENSMUSG00000045098" "ENSMUSG00000024598"
[6] "ENSMUSG00000028023"

[Jens von Preußen]

It seems that c.view.pathways by default applies row ordering. There is a parameter row.order available, which seems to take in an ordering of the provided gene name. Maybe you can add a bit of documentation to the c.view.pathway method :)

Best,
Jens

[jeanfanph...@gmail.com]

Thanks Jens! 

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