[BioC] Retrieving KEGG pathway diagrams via KEGGSOAP

Daren Tan darentan76 at gmail.com
Fri Apr 17 10:47:44 CEST 2009


Grateful for the help. Now I can get some nice KEGG pictures. On hand,
I have about 20 pathways for visualization, how can I download the 20
gifs or possibly higher resolution pictures and collate them into a
pdf ? Possible to do all these steps via R ?

On Fri, Apr 17, 2009 at 10:02 AM, Saroj K Mohapatra <smohapat at vbi.vt.edu> wrote:
> Hi Daren,
>
> I do not know why but if you try with more than one node, the code works.
>
>> url <- mark.pathway.by.objects("path:hsa03050",
>  c("hsa:5709", "hsa:10197"))
>
>> url
> [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api15820/hsa03050.gif"
>
>> if(interactive()){ browseURL(url) }
>
> Best,
>
> Saroj
>
>
> ----- Original Message -----
> From: "Daren Tan" <darentan76 at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Sent: Thursday, April 16, 2009 8:46:30 PM GMT -05:00 US/Canada Eastern
> Subject: [BioC] Retrieving KEGG pathway diagrams via KEGGSOAP
>
> There was an earlier example about KEGGSOAP, which I am looking for
> all this while. My work centers around hsa, so I tried one of the
> pathway annotated in human and sound genes. However, NULL is always
> returned. What is wrong ?
>
>> get.genes.by.pathway("path:hsa03050")
>  [1] "hsa:100132108" "hsa:10197"     "hsa:10213"     "hsa:121906"
> "hsa:122706"    "hsa:143471"    "hsa:23198"     "hsa:345645"
> "hsa:3458"
> [10] "hsa:51371"     "hsa:5682"      "hsa:5683"      "hsa:5684"
> "hsa:5685"      "hsa:5686"      "hsa:5687"      "hsa:5688"
> "hsa:5689"
> [19] "hsa:5690"      "hsa:5691"      "hsa:5692"      "hsa:5693"
> "hsa:5694"      "hsa:5695"      "hsa:5696"      "hsa:5698"
> "hsa:5699"
> [28] "hsa:5700"      "hsa:5701"      "hsa:5702"      "hsa:5704"
> "hsa:5705"      "hsa:5706"      "hsa:5707"      "hsa:5708"
> "hsa:5709"
> [37] "hsa:5710"      "hsa:5713"      "hsa:5714"      "hsa:5717"
> "hsa:5718"      "hsa:5719"      "hsa:5720"      "hsa:5721"
> "hsa:652826"
> [46] "hsa:7979"      "hsa:9491"      "hsa:9861"
>> url <- mark.pathway.by.objects("path:hsa03050", "hsa:10197")
>> url
> NULL
>> url <- mark.pathway.by.objects("path:hsa03050", "hsa:5684")
>> url
> NULL
>
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] KEGGSOAP_1.16.0 SSOAP_0.4-6     RCurl_0.94-1    XML_2.1-0
> limma_2.16.4    RSQLite_0.7-1   DBI_0.2-4
>
> loaded via a namespace (and not attached):
> [1] gdata_2.4.2    gplots_2.6.0   gtools_2.5.0-1 tools_2.8.1
>
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> --
> Computational Biology
> VBI @ Virginia Tech
>



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