Retrieving KEGG pathway diagrams via KEGGSOAP

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Daren Tan ▴ 120

@daren-tan-3309

Last seen 10.3 years ago

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

KEGGSOAP KEGGSOAP • 1.4k views

ADD COMMENT • link updated 15.7 years ago by Paolo Sonego ▴ 140 • written 15.7 years ago by Daren Tan ▴ 120

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Saroj Mohapatra ▴ 450

@saroj-mohapatra-1446

Last seen 10.3 years ago

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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology VBI @ Virginia Tech

ADD COMMENT • link 15.7 years ago Saroj Mohapatra ▴ 450

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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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Computational Biology > VBI @ Virginia Tech >

ADD REPLY • link 15.7 years ago Daren Tan ▴ 120

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Paolo Sonego ▴ 140

@paolo-sonego-3256

Last seen 10.3 years ago

Italy

Dear Daren, If you are in a Unix environment (Linux/Mac OS X), below there is a trivial example taking advantage of EBImage package and ImageMagick toolkit (sorry I can figure out how to use EBImage to combine the different images in a single pdf). library(KEGGSOAP) url <- mark.pathway.by.objects("path:hsa03050", c("hsa:5709", "hsa:10197")) urls <- c(url, url, url) ## set different urls here library(EBImage) im.gif <- NULL for (i in 1:length(urls)){ im.gif <- readImage(urls[i], TrueColor) writeImage(im.gif, paste("pathway_", i, ".pdf", sep="")) } to combine the files in a single pdf: system("convert pathway_* pathways.pdf") HIH. Paolo

ADD COMMENT • link 15.7 years ago Paolo Sonego ▴ 140

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