[BioC] Pathview - Problem with PNG output

[Luo Weijun]

Christian,
I run a similar job with the following lines, pathview works fine.
ko.data=sim.mol.data(mol.type="gene.ko", nmol=5000)
pv.out <- pathview(gene.data = ko.data, pathway.id = "01040",
                   species = "ko", out.suffix = "ko.data", kegg.native = T)

The fact that no up/down regulated genes show up could be because there is really no gene mapped into this pathway at all or no genes in this pathway are actually up/down regulated. Have you checked to make sure these two possibilities are excluded?
BTW, I can’t reproduce your Warning message either. If you still have problem, please email me your own data plus the output of sessionInfo(). I will see whether I can reproduce it.
Weijun


--------------------------------------------
On Fri, 9/20/13, Christian De Santis <christian.desantis at stir.ac.uk> wrote:


Hi everyone,

I am running a KEGG analysis using Pathview to visualize my results. Everything works fine. However, for one of my pathway (01040 - Fatty Acid Biosynthesis), it fails to associate the values to the graph so that the png output does not show the genes that are up/down regulated. The code I run is the following:

pv.out.03050 <- pathview(gene.data = KO.BPC.fit.gd [,4], pathway.id = "03050", species = "ko", out.suffix = "BPC.proteasome", kegg.native = T)
pv.out.01040 <- pathview(gene.data = KO.BPC.fit.gd [,4], pathway.id = "01040", species = "ko", out.suffix = "BPC.FA.BIOS", kegg.native = T)

but I think it Is irrelevant since the first code, which is exactly the same as the second, works fine. Does anyone have any clue what the problem could be?

Also, for both codes I get the following warning message (although it does not seem to affect the output of the first code):

> pv.out.03050 <- pathview(gene.data = KO.BPC.fit.gd [,4], pathway.id = "03050", species = "ko", out.suffix = "BPC.proteasome", kegg.native = T)
[1] "Downloading xml files for ko03050, 1/1 pathways.."
[1] "Downloading png files for ko03050, 1/1 pathways.."
Working in directory H:/My Documents/R_Analyses/TSB/Screening
Writing image file ko03050.BPC.proteasome.png
Warning message:
In download.file(xml.url, xml.target, quiet = T) :
  downloaded length 14985 != reported length 200

Any help would be kindly appreciated,
Best Regards,
Christian

-- 
The University of Stirling has been ranked in the top 12 of UK universities for graduate employment*.
94% of our 2012 graduates were in work and/or further study within six months of graduation.
*The Telegraph
The University of Stirling is a charity registered in Scotland, number SC 011159.