Rgraphviz, deprecated imageMap
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@ariel-chernomoretz-1863
Last seen 7 months ago
Argentina
Hi BioC's and Rgraphviz maintainers, I have recently installed BioC 2.1 on R 2.6 and I found that the imageMap function is not included anymore in Rgraphviz 1.16. I found that function real handy to produce visual reports of GO overrepresentation analysis performed mainly with GOstats. (As a matter of fact I was in the process of cleaning the code in order to submit a new bioc tool intended to produce fancy html reports) Is there any chance to reconsider including the imageMap functionality again in Rgraphviz? Thanks Ariel./
Rgraphviz PROcess GOstats Rgraphviz PROcess GOstats • 1.1k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 8.9 years ago
United States
Hi, FYI in R and BioC you will know if a function is deprecated or not by the error/warning you get when you try to use it, and typically such a warning will be present for about six months before the function is made defunct. In this case no such deprecation has happened. imageMap is in the geneplotter package. best wishes Robert Ariel Chernomoretz wrote: > Hi BioC's and Rgraphviz maintainers, > > I have recently installed BioC 2.1 on R 2.6 and I found that the > imageMap function is not included anymore in > Rgraphviz 1.16. > I found that function real handy to produce visual reports of GO > overrepresentation analysis performed mainly with GOstats. > (As a matter of fact I was in the process of cleaning the code in > order to submit a new bioc tool intended to produce > fancy html reports) > > Is there any chance to reconsider including the imageMap functionality > again in Rgraphviz? > Thanks > Ariel./ > > _______________________________________________ > 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 > -- 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
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Hi Robert, Thanks for your quick answer. The problem is that Rgraphviz sets in fact a new method to the generic function 'imageMap' from geneplotter, that accept an Ragraph object (and not a matrix with boxplot coordinates) as the first argument . Regards Ariel./ On Nov 26, 2007 1:32 PM, Robert Gentleman <rgentlem at="" fhcrc.org=""> wrote: > Hi, > > FYI in R and BioC you will know if a function is deprecated or not by > the error/warning you get when you try to use it, and typically such a > warning will be present for about six months before the function is made > defunct. In this case no such deprecation has happened. > > imageMap is in the geneplotter package. > > best wishes > Robert > > > > Ariel Chernomoretz wrote: > > Hi BioC's and Rgraphviz maintainers, > > > > I have recently installed BioC 2.1 on R 2.6 and I found that the > > imageMap function is not included anymore in > > Rgraphviz 1.16. > > I found that function real handy to produce visual reports of GO > > overrepresentation analysis performed mainly with GOstats. > > (As a matter of fact I was in the process of cleaning the code in > > order to submit a new bioc tool intended to produce > > fancy html reports) > > > > Is there any chance to reconsider including the imageMap functionality > > again in Rgraphviz? > > Thanks > > Ariel./ > > > > _______________________________________________ > > 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 > > > > -- > 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 >
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Hi Ariel, Ariel Chernomoretz wrote: > Hi Robert, > > Thanks for your quick answer. > The problem is that Rgraphviz sets in fact a new method to > the generic function 'imageMap' from geneplotter, that accept an Ragraph object > (and not a matrix with boxplot coordinates) as the first argument . It seems that this method has been moved to the biocGraph package. Cheers, H.
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Thanks! a./ On Nov 26, 2007 4:07 PM, Herve Pages <hpages at="" fhcrc.org=""> wrote: > Hi Ariel, > > Ariel Chernomoretz wrote: > > Hi Robert, > > > > Thanks for your quick answer. > > The problem is that Rgraphviz sets in fact a new method to > > the generic function 'imageMap' from geneplotter, that accept an Ragraph object > > (and not a matrix with boxplot coordinates) as the first argument . > > It seems that this method has been moved to the biocGraph package. > > Cheers, > H. >
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