[BioC] GO graph plotting with some in color

[Robert Gentleman]

Loren Engrav wrote:
> Followup to this issue
> 
> I can move the color data from Excel to BBedit
> Then edit till I have the string like GO:0004198="red", GO:004199="blue"
> Then copy paste into the c function and the error below does not occur and I
> obtain red and blue nodes, which is cool

   If you read the documentation for the function you are trying to use, 
it will explain the format of the arguments.  In this case you need a 
named vector.  You can also evaluate the examples and see what was used 
to create them.

   If you then look at what you get when you read in the data from a 
file, as you have described, you will see it is not a named vector, and 
you will need to process it to get the form needed to pass on to the 
plotting routines.

   Perhaps the easiest way is to replace the = in your file with a comma 
or some other delimiter (or use the sep argument in the 
read.table/read.delim family of functions - lots of documentation here 
too, ?read.delim) and read in the data as a data.frame. Then use that to 
create the named vector.


> 
> This may be good enough. But can I set up a text file in some form and then
> read or scan or something the data in?
> 
> I have tried scan and read.delim and googled, etc but have failed
> 
> Thank you
> =========================================
> 
>> From: Loren Engrav <engrav at u.washington.edu>
>> Date: Fri, 23 Nov 2007 13:31:32 -0800
>> To: <bioconductor at stat.math.ethz.ch>
>> Conversation: GO graph plotting with some in color
>> Subject: [BioC] GO graph plotting with some in color
>>
>>
>> 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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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org