Hello, I can use the "mark.pathway.by.objects" function in KEGGSOAP to mark objects in a KEGG pathway. That is, the objects I mark in the "object.id.list" show up on the generated KEGG pathway. However, the "color.pathway.by.objects" does not seem to work (at least the way I am thinking it should). Specifically, the colors for "fg.color.list" and "bg.color.list" stay the same no matter what color I put in there. I can see no difference in the pathway that is generated. Here is a small example: Using a slightly modified example from the "mark.pathway.by.objects" help page, the following three codings all give the same colors for the marked up objects, and the pathways all look the same. if(require("SSOAP") && require("XML")){ url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:b0003")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:b0003"), c("#ff0000", "#00ff00"), c("#ffff00","yellow")) } ########################################### if(require("SSOAP") && require("XML")){ url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:b0003")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:b0003"), c("red", "blue"),c("#ffff00","yellow")) } ############################################# if(require("SSOAP") && require("XML")){ url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:b0003")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:b0003"), c("yellow", "orange"),c("red","blue")) } ################################################# > sessionInfo() R version 2.5.1 (2007-06-27) 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: KEGGSOAP SSOAP RCurl XML "1.10.0" "0.4-3" "0.8-0" "1.9-0" Alex Cambon Biostatistician Dept of Bioinformatics and Biostatistics School of Public Health and Information Sciences University of Louisville 502-852-4111 accamb01 at louisville.edu

> >However, the "color.pathway.by.objects" does not seem to work (at least the way I am thinking it should). Specifically, the colors for "fg.color.list" and "bg.color.list" stay the same no matter what color I put in there. I can see no difference in the pathway that is generated. KEGGSOAP is merely an interface to KEGG's API without any data processing or display. I checked the parameters of the function against KEGG's API and did not see anything wrong. I wonder if anyone has tried to do the same using KEGG's API throuhg other approaches (e. g. using Java ...) and got it to work? > >Here is a small example: > >Using a slightly modified example from the "mark.pathway.by.objects" help page, the following three codings all give the same colors for the marked up objects, and the pathways all look the same. > > if(require("SSOAP") && require("XML")){ > url <- mark.pathway.by.objects("path:eco00260", > c("eco:b0002", "eco:b0003")) > if(interactive()){ > browseURL(url) > } > url <- color.pathway.by.objects("path:eco00260", > c("eco:b0002", "eco:b0003"), > c("#ff0000", "#00ff00"), c("#ffff00","yellow")) > > > } > > >########################################### > > if(require("SSOAP") && require("XML")){ > url <- mark.pathway.by.objects("path:eco00260", > c("eco:b0002", "eco:b0003")) > if(interactive()){ > browseURL(url) > } > url <- color.pathway.by.objects("path:eco00260", > c("eco:b0002", "eco:b0003"), > c("red", "blue"),c("#ffff00","yellow")) > > } > >############################################# > > if(require("SSOAP") && require("XML")){ > url <- mark.pathway.by.objects("path:eco00260", > c("eco:b0002", "eco:b0003")) > if(interactive()){ > browseURL(url) > } > url <- color.pathway.by.objects("path:eco00260", > c("eco:b0002", "eco:b0003"), > c("yellow", "orange"),c("red","blue")) > > } > >################################################# >> sessionInfo() >R version 2.5.1 (2007-06-27) >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: >KEGGSOAP SSOAP RCurl XML >"1.10.0" "0.4-3" "0.8-0" "1.9-0" > >Alex Cambon >Biostatistician >Dept of Bioinformatics and Biostatistics >School of Public Health and Information Sciences >University of Louisville >502-852-4111 >accamb01 at louisville.edu > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084