Hi, I tried the code from a previous post: ------------ url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263"), c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))--------------- Is there any way to make the all the initial nodes as 'white' (instead of light green), and then to color the nodes that we are interested in? thanks! [[alternative HTML version deleted]]

Hi Tim: It is possible to set the foreground and background colors for each node in the KEGG pathway through bg.color.list and fg.color.list arguments of the function color.pathway.by.objects. I color just one node below in white-on-blue, rest all in black-on-white. > library("KEGGSOAP") Loading required package: XML Loading required package: SSOAP Loading required package: RCurl # Suppose you are looking at the pathway for glycolysis / gluconeogenesis > pathstr = "path:hsa00010" # get all genes > glist = get.genes.by.pathway(pathstr) # First fix what color you want for which node # Suppose, you want to color first enzyme hsa:10327 (EC 1.1.1.2) # white on blue background and rest all nodes in black on white # fgcols = color of text and border # bgcols = color of the rectangular area > fgcols = rep("black", length(glist)) > fgcols[1] = "yellow" > bgcols = rep("white", length(glist)) > bgcols[1] = "blue" # color the pathway accordingly > url = color.pathway.by.objects(pathstr, glist, fg=fgcols, bg=bgcols) # Have a look at the url returned > url [1] "http://soap.genome.jp/tmp/mark_pathway_www3_api23663/hsa00010.gif" > browseURL(url) > > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGGSOAP_1.14.0 SSOAP_0.4-6 RCurl_0.94-1 XML_2.3-0 > > Best wishes, Saroj ----- Original Message ----- From: "Tim Smith" <tim_smith_666@yahoo.com> To: "bioc" <bioconductor at="" stat.math.ethz.ch=""> Sent: Friday, April 17, 2009 6:19:59 PM GMT -05:00 US/Canada Eastern Subject: [BioC] Visualize KEGG pathway Hi, I tried the code from a previous post: ------------ url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263"), c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))--------------- Is there any way to make the all the initial nodes as 'white' (instead of light green), and then to color the nodes that we are interested in? thanks! [[alternative HTML version deleted]] _______________________________________________ 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

Hi Tim Check out section 3 of the sample code on our website: http://www.iah.ac.uk/research/bioinformatics/bioinf1.shtml#Code Thanks Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Tim Smith Sent: Fri 17/04/2009 11:19 PM To: bioc Subject: [BioC] Visualize KEGG pathway Hi, I tried the code from a previous post: ------------ url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263"), c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))--------------- Is there any way to make the all the initial nodes as 'white' (instead of light green), and then to color the nodes that we are interested in? thanks! [[alternative HTML version deleted]] _______________________________________________ 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