I got it. To plot a GOgraph output, you need
Rgraphviz
geneplotter
My plot now looks reasonable. Thanks, Jim.
Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348
(Statistics)
University Park, PA 16802-2111
Naomi Altman <naomi at="" stat.psu.edu=""> writes:
> I am starting to use GOstat, and there are several things I do not
> understand.
Please let me know what parts are not clear. I would like to improve
the documentation and make the code as easy to use as possible.
> I managed to get output from HyperGTest. I was able to view the
> enriched categories using htmlReport.
>
> I would like to try out the graphing methods, but I have not been
> able to figure out the input. In particular, I assume that since I
> have created a GOHyperGResult object, I should use
The plot methods in GOstats are not very refined. In part, this is
because it isn't always clear what picture one should draw.
So suggestions here would be welcome.
For example, given the result of a hyperGtest, one could plot all GO
terms significant at a specified p-value and show their relationships.
But that is a rather incomplete picture. OTOH, if you expand the
graph by very much it becomes useless as you can't see anything once
you plot 100 nodes at once.
> getGoGraph
>
> but I have not figured out what goes into the goIds argument. I
> presume it is some type of node identifier, but where do I find it?
goIds should be a character vector of GO IDs, like "GO:xxxxxx".
+ seth
Hi Seth,
Seth Falcon wrote:
> Naomi Altman <naomi at="" stat.psu.edu=""> writes:
>
>
>>I am starting to use GOstat, and there are several things I do not
>>understand.
>
>
> Please let me know what parts are not clear. I would like to
improve
> the documentation and make the code as easy to use as possible.
>
>
>>I managed to get output from HyperGTest. I was able to view the
>>enriched categories using htmlReport.
>>
>>I would like to try out the graphing methods, but I have not been
>>able to figure out the input. In particular, I assume that since I
>>have created a GOHyperGResult object, I should use
>
>
> The plot methods in GOstats are not very refined. In part, this is
> because it isn't always clear what picture one should draw.
>
> So suggestions here would be welcome.
>
> For example, given the result of a hyperGtest, one could plot all GO
> terms significant at a specified p-value and show their
relationships.
> But that is a rather incomplete picture. OTOH, if you expand the
> graph by very much it becomes useless as you can't see anything once
> you plot 100 nodes at once.
>
>
>>getGoGraph
>>
>>but I have not figured out what goes into the goIds argument. I
>>presume it is some type of node identifier, but where do I find it?
>
>
> goIds should be a character vector of GO IDs, like "GO:xxxxxx".
Consider the following code:
library(hgu133plus2)
library(GOstats)
library(Rgraphviz)
lls <- unlist(as.list(hgu133plus2ENTREZID))[1:500]
lls <- lls[!is.na(lls)]
univ <- unlist(as.list(hgu133plus2ENTREZID))
univ <- univ[!is.na(univ)]
params <- new("GOHyperGParams", geneIds=lls, universeGeneIds=univ,
ontology="BP", annotation="hgu133plus2", conditional=TRUE)
hypt <- hyperGTest(params)
grph1 <- getGoGraph(params, summary(hypt)[1:3,1])
plot(grph1)
grph2 <- GOGraph(summary(hypt)[1:3,1], GOBPPARENTS)
plot(grph2)
Is the intent that the two graphs should be identical? My reading of
the
help page leads me to believe so.
Best,
Jim
>
> + seth
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Yup. You responded about 10 milliseconds before I was going to hit
'Send' on an email saying just that ;-D. Category suggests Rgraphviz,
but it isn't a dependency, so I guess is not automatically loaded.
Best,
Jim
Naomi Altman wrote:
> I got it. To plot a GOgraph output, you need
>
> Rgraphviz
> geneplotter
>
> My plot now looks reasonable. Thanks, Jim.
>
>
> Naomi S. Altman 814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics 814-863-7114 (fax)
> Penn State University 814-865-1348
(Statistics)
> University Park, PA 16802-2111
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
