[BioC] GO graph plotting with some in color

[Loren Engrav]

Cool, thank you

After 11 days 
I can read in the data and have the graph
That is a rather expensive graph I would say :)

> nAttrs = list()
> colors  <-  scan(file="339colorsRowBB.txt", what="character")
Read 339 items
> names(colors)  <-  scan(file="339namesRowBB.txt", what="character")
Read 339 items
> nAttrs$fillcolor  <- colors
> nAttrs$color  <-  colors

> bpCutLeaves <- scan(file="339namesRowBB.txt", what = "character")
Read 339 items
> bpCutLeavestree <- GOGraph(bpCutLeaves, GOBPPARENTS)
> postscript ("bpCutLeavestree.ps", width=100, height = 100, paper="special");
plot (bpCutLeavestree, nodeAttrs=nAttrs); dev.off()
postscript 
         2 


Graph is up at <http://homepage.mac.com/engrav/Menu9.html> and hit arrow on
FileSharing

Now I have 3 questions please

1) the code above reads in two files, one for colors and one for names; that
seems rather grade school, is there not a more efficient way, like with one
file

2) in the graph the colored and therefore "significant" nodes have no
incoming edges from other colored and "significant" nodes; is it possible
that none of the 339 "significant" nodes have a parent within the 339?

3) and finally, What do I have?  We are getting enrichment from DAVID and
Amigo as they are lots more user friendly than Bioconductor. But they fail
at plotting so I tried Bioconductor.  The resultant graph shows red and blue
sprinkled here and there but so what?

I found a manuscript with an almost identical graph with credits to
Bioconductor.  See Journal of Molecular Endocrinology (2006) 37, 301­316.  I
checked their conclusions from the graph and found them rather skimpy.

What is the conclusion from the graph? Or is it just a pretty graph?  But it
was fun, by the way.

Again thank you for helping.  I am grateful.

Loren Engrav
Univ Wash
Seattle, WA USA  


> From: Robert Gentleman <rgentlem at fhcrc.org>
> Date: Mon, 26 Nov 2007 11:33:58 -0800
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] GO graph plotting with some in color
> 
> 
> 
> 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