Hello! I have this problem: I want to create a Venn's diagram with three lists of genes'names. The first is all the genome, the second a subset of it comprising all mitochondrial genes, and the third including all genes that correlate with a given gene. This is what I do:> library(gplots) > A<-read.delim("F:/.../mito genes just names.txt") > B<-read.delim("F:/.../My gene all cors names.txt") > C<-read.delim("F:/.../all genes names.txt") > input<-list(A,B,C) > venn(input)However, the output is empty, being no number inside each intersection. I think the issue lyes in the non-numeric nature of the list, but I don't know if a solution for this exists... If anybody can help, this would be a great thing. Thanks! Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov
Gabriele, Take a look at this: http://research.stowers-institute.org/efg/R/Math/VennDiagram.htm Best, Jorge On Sat, Jan 30, 2010 at 10:13 PM, Zoppoli, Gabriele (NIH/NCI) [G] <> wrote:> Hello! > > I have this problem: I want to create a Venn's diagram with three lists of > genes'names. The first is all the genome, the second a subset of it > comprising all mitochondrial genes, and the third including all genes that > correlate with a given gene. > > This is what I do: > > > library(gplots) > > A<-read.delim("F:/.../mito genes just names.txt") > > B<-read.delim("F:/.../My gene all cors names.txt") > > C<-read.delim("F:/.../all genes names.txt") > > input<-list(A,B,C) > > venn(input) > > However, the output is empty, being no number inside each intersection. I > think the issue lyes in the non-numeric nature of the list, but I don't know > if a solution for this exists... > > If anybody can help, this would be a great thing. > > Thanks! > > > Gabriele Zoppoli, MD > Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University > of Genova, Genova, Italy > Guest Researcher, LMP, NCI, NIH, Bethesda MD > > Work: 301-451-8575 > Mobile: 301-204-5642 > Email: > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
On 01/31/2010 02:13 PM, Zoppoli, Gabriele (NIH/NCI) [G] wrote:> Hello! > > I have this problem: I want to create a Venn's diagram with three lists of genes'names. The first is all the genome, the second a subset of it comprising all mitochondrial genes, and the third including all genes that correlate with a given gene. > > This is what I do: > >> library(gplots) >> A<-read.delim("F:/.../mito genes just names.txt") >> B<-read.delim("F:/.../My gene all cors names.txt") >> C<-read.delim("F:/.../all genes names.txt") >> input<-list(A,B,C) >> venn(input) > > However, the output is empty, being no number inside each intersection. I think the issue lyes in the non-numeric nature of the list, but I don't know if a solution for this exists... >Hi Gabriele, As I don't have the data, I can't be sure, but are the names consistent across the three files? That is, I suspect that there may be prefixes or suffixes that designate different classes (e.g. "m" for mitochondrial). Jim