[BioC] KEGGSOAP: color.pathway.by.objects

[Alexander C Cambon]

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