Thank you very much David!

Following your hint I learned to set the attributes using the following 
code:

nA <- makeNodeAttrs(mapkG, label=nodesNames, fixedsize=F,  width=20, 
height=20, font=20, fontsize=20)
plot(mapkG, "dot", nodeAttrs=nA)

Unfortunately, changing he height/width or fontsize (after setting 
fixedsize to FALSE) does not change the output.

Best wishes

Kristian


On 16/12/10 16:14, Jitao David Zhang wrote:
> Hi dear Kristian,
>
>   Try 'makeNodeAttrs' function (Rgraphviz). If you are interested, you 
> can have a look at the source file (Rnw) of KEGGGgraphApp.Rnw shipped 
> along with the KEGGgraph package (/inst/doc/KEGGgraphApp.Rnw), there 
> you may find how to use it.
>
>   For the width and height, some experience suggests that 'fixedsize' 
> option of nodeAttrs could be tweaked.
>
>   If you had further questions, please feel free to attach a souce 
> code which one could test and we could see how it works.
>
>   Best wishes,
> David
>
>
>
> 2010/12/16 Unger, Kristian <k.unger@imperial.ac.uk 
> <mailto:k.unger@imperial.ac.uk>>
>
>     Hi there
>
>     I am trying to optimise an output of pathway analysis and I am halfway
>     successful doing this using KEGGgraph. The most useful layout for my
>     purposes is the "dot" layout. The only problem I have is that I cannot
>     change the layout parameters for the nodes such as 'width',
>     'height' or
>     anything.
>
>     Please find the code I am using in the following:
>
>     nAttrs <- list();
>     nAttrs$fillcolor <- makeAttr(mapkG, "lightgrey",
>     list(green=as.character(merge[,1]),red=as.character(merge2[,1])
>                     ,yellow=as.character(merge3[,1])))#green=n[1:5]))
>     #merge1,2 and 3 are strings of KEGG gene IDs which appear green,
>     red and
>     yellow in the plot
>     nAttrs$label <- nodesNames
>
>     nAttrs$height <-"3"
>     names(nAttrs$height) <- "height"
>     nAttrs$fontsize <- "20"
>     names(nAttrs$fontsize) <- "fontsize"
>
>     plot(mapkG, "dot", nodeAttrs=nAttrs)
>
>     I tried to set the node attributes height and fontsize by writing the
>     values into nAttrs$height and nAttrs$fontsize. Doing this an error
>     message ('Error in buildNodeList(graph, nodeAttrs, subGList,
>     attrs$node)
>     :  the character vector must have names") came up. I added the
>     names and
>     the plot was generated without any errors but there still was not any
>     effect on height and fontsize of the nodes.
>
>     It would be great if someone could give me some ideas on this!
>
>     Best wishes
>
>     Kristian
>
>     > sessionInfo()
>     R version 2.11.1 (2010-05-31)
>     i686-pc-linux-gnu
>
>     locale:
>      [1] LC_CTYPE=en_GB.utf8          LC_NUMERIC=C
>      [3] LC_TIME=en_GB.utf8           LC_COLLATE=en_GB.utf8
>      [5] LC_MONETARY=en_GB.utf8       LC_MESSAGES=en_GB.utf8
>      [7] LC_PAPER=en_GB.utf8          LC_NAME=en_GB.utf8
>      [9] LC_ADDRESS=en_GB.utf8        LC_TELEPHONE=en_GB.utf8
>     [11] LC_MEASUREMENT=en_GB.utf8    LC_IDENTIFICATION=en_GB.utf8
>
>     attached base packages:
>     [1] grid      stats     graphics  grDevices utils     datasets
>      methods
>     [8] base
>
>     other attached packages:
>      [1] biomaRt_2.4.0        KEGGgraph_1.4.0      XML_3.2-0
>      [4] org.Hs.eg.db_2.4.1   RSQLite_0.9-4        DBI_0.2-5
>      [7] AnnotationDbi_1.10.2 Biobase_2.8.0        Rgraphviz_1.26.0
>     [10] graph_1.28.0         rj_0.5.0-5
>
>     loaded via a namespace (and not attached):
>     [1] RCurl_1.4-3  rJava_0.8-7  tools_2.11.1
>
>
>     --
>     _____
>
>     Dr Kristian Unger
>
>     Imperial College London
>
>
>
>
>            [[alternative HTML version deleted]]
>
>     _______________________________________________
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>     Bioconductor@r-project.org <mailto:Bioconductor@r-project.org>
>     https://stat.ethz.ch/mailman/listinfo/bioconductor
>     Search the archives:
>     http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
> -- 
> Jitao David Zhang
> Pre-doc staff of Computational Biology and Biostatistics
> Division of Molecular Genome Analysis
> DKFZ, Heidelberg D-69120, Germany
>
> http://www.NextBioMotif.com/

-- 
_____

Dr Kristian Unger

Bioinformaticist Chernobyl Tissue Bank

Department of Surgery and Cancer

Imperial College London

Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS

Tel +44-20-8383-2443

Mob +44-795-1080619

http://www1.imperial.ac.uk/medicine/people/k.unger/
http://www.chernobyltissuebank.com



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