[BioC] GO graph plotting with some in color

Loren Engrav engrav at u.washington.edu
Fri Nov 23 22:31:32 CET 2007


So am doing GO graphing and I have done

> bpCutLeaves <- scan(file="343afterDupesNotCut.txt", what = "character")
Read 343 items
> bpCutLeavestree <- GOGraph(bpCutLeaves, GOBPPARENTS)
> postscript ("bpCutLeavestreeTest.ps", width=100, height = 100,
paper="special"); plot (bpCutLeavestree); dev.off()
quartz 
     2 
> bpCutLeavestree
A graphNEL graph with directed edges
Number of Nodes = 1456
Number of Edges = 2418

And the postscript file is very nice
But I need the 343 leaves colored red (over expression) and blue (under
expression)

So from Rgraphviz documentation I do
 
> nAttrs  <-  list()
> nAttrs$color <- scan(file="343forColorBB.txt", what="character")
Read 343 items
> nAttrs$fillcolor <- scan(file="343forColorBB.txt", what="character")
Read 343 items

Where in 343ForColorBB.txt I set the 343 to red or blue, it is a text file
with 343 items like GO:0000002="red"

Then I do
> postscript ("bpCutLeavestreeTest.ps", width=100, height = 100,
paper="special"); plot (bpCutLeavestree, nodeAttrs = nAttrs); dev.off()

But it returns

Error in buildNodeList(graph, nodeAttrs, subGList, attrs$node) :
  the character vector must have names

I am stuck...
What have I left out

Thank you

Loren Engrav
Univ Wash
Seattle



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