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

[John Zhang]

>
>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
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084