venn diagrams
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David Lyon ▴ 340
@david-lyon-4016
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Sorry newbie question. If I had 6 files named 1,2,3,4 each file containing a ID eg: ENST00000326632 etc. Can someone provide the code that loads each file and generates a Venn Diagram displaying the intersection/unique/union of the data sets in both a table format and a diagramatic format like a jpeg ? Thanks in advance.
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@thomas-hampton-2820
Last seen 9.6 years ago
You might try gplots: venn package:gplots R Documentation Plot a Venn diagram Description: Plot Venn diagrams for up to 5 sets Usage: venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE, simplify=FALSE, show.plot=TRUE) best, Tom On Jun 2, 2010, at 3:48 PM, David Lyon wrote: > Sorry newbie question. > > If I had 6 files named 1,2,3,4 each file containing a ID eg: > > ENST00000326632 > etc. > > Can someone provide the code that loads each file and generates a > Venn Diagram displaying the intersection/unique/union of the data > sets in both a table format and a diagramatic format like a jpeg ? > > Thanks in advance. > > _______________________________________________ > 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
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Thanks Thomas can you or someone give me a clue on how to load the files and then generate a venn diagram and the various data sets that lists the union/intesect/unique members. I have read the gplots but its not clear to me as a newbie. ----- Original Message ---- From: Thomas Hampton <thomas.h.hampton@dartmouth.edu> To: David Lyon <david_lyon3 at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Wed, June 2, 2010 4:03:07 PM Subject: Re: [BioC] venn diagrams You might try gplots: venn package:gplots R Documentation Plot a Venn diagram Description: Plot Venn diagrams for up to 5 sets Usage: venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE, simplify=FALSE, show.plot=TRUE) best, Tom On Jun 2, 2010, at 3:48 PM, David Lyon wrote: > Sorry newbie question. > > If I had 6 files named 1,2,3,4 each file containing a ID eg: > > ENST00000326632 > etc. > > Can someone provide the code that loads each file and generates a Venn Diagram displaying the intersection/unique/union of the data sets in both a table format and a diagramatic format like a jpeg ? > > Thanks in advance. > > _______________________________________________ > 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
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You can try overLapper function in BioC instruction. It will do up to five lists. Steve On Wed, Jun 2, 2010 at 5:10 PM, David Lyon <david_lyon3@yahoo.com> wrote: > Thanks Thomas > > can you or someone give me a clue on how to load the files and then > generate a venn diagram and the various data sets that lists the > union/intesect/unique members. I have read the gplots but its not clear to > me as a newbie. > > > > > > > ----- Original Message ---- > From: Thomas Hampton <thomas.h.hampton@dartmouth.edu> > To: David Lyon <david_lyon3@yahoo.com> > Cc: bioconductor@stat.math.ethz.ch > Sent: Wed, June 2, 2010 4:03:07 PM > Subject: Re: [BioC] venn diagrams > > You might try gplots: > > venn package:gplots R Documentation > > Plot a Venn diagram > > Description: > > Plot Venn diagrams for up to 5 sets > > Usage: > > venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE, > simplify=FALSE, show.plot=TRUE) > > best, > > Tom > > On Jun 2, 2010, at 3:48 PM, David Lyon wrote: > > > Sorry newbie question. > > > > If I had 6 files named 1,2,3,4 each file containing a ID eg: > > > > ENST00000326632 > > etc. > > > > Can someone provide the code that loads each file and generates a Venn > Diagram displaying the intersection/unique/union of the data sets in both a > table format and a diagramatic format like a jpeg ? > > > > Thanks in advance. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Thanks Steve I used this tutorial: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_graphics_ venn which clearly demonstrates how to use OverLapper. I only wished that all the packages from R and bioconductor could be written with the clarity and simplicity as the tutorial above..... ________________________________ From: Steve Shen <sshen@bu.edu> Cc: Thomas Hampton <thomas.h.hampton@dartmouth.edu>; bioconductor@stat.math.ethz.ch Sent: Wed, June 2, 2010 6:51:04 PM Subject: Re: [BioC] venn diagrams You can try overLapper function in BioC instruction. It will do up to five lists. Steve Thanks Thomas > >>can you or someone give me a clue on how to load the files and then generate a venn diagram and the various data sets that lists the union/intesect/unique members. I have read the gplots but its not clear to me as a newbie. > > > > > > >>----- Original Message ---- >>From: Thomas Hampton <thomas.h.hampton@dartmouth.edu> >>Cc: bioconductor@stat.math.ethz.ch >>Sent: Wed, June 2, 2010 4:03:07 PM >>Subject: Re: [BioC] venn diagrams > >>You might try gplots: > >>venn package:gplots R Documentation > >>Plot a Venn diagram > >>Description: > >> Plot Venn diagrams for up to 5 sets > >>Usage: > >> venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE, >> simplify=FALSE, show.plot=TRUE) > >>best, > >>Tom > >>On Jun 2, 2010, at 3:48 PM, David Lyon wrote: > >>> Sorry newbie question. >>> >>> If I had 6 files named 1,2,3,4 each file containing a ID eg: >>> >>> ENST00000326632 >>> etc. >>> >>> Can someone provide the code that loads each file and generates a Venn Diagram displaying the intersection/unique/union of the data sets in both a table format and a diagramatic format like a jpeg ? >>> >>> Thanks in advance. > >> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>_______________________________________________ >>Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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David Lyon ▴ 340
@david-lyon-4016
Last seen 2.4 years ago
United States
Does anyone know the answer to this simple question library(gplots) This works great from the console: A <- c(1,2,3,4) B <- c(1,2,3,4) C <- c(1,2,3,4) input<-list(A,B,C) venn(input) When I input the data from flat files each containing in a single col it is only using the first row from each file in the venn diagram eg: A <- ("A.file") B <- ("B.file") C <- ("C.file") input<-list(A,B,C) venn(input) its returns the venn diagram from only the first row from each file , how do I change the code so it uses every data point in each column. Thanks contents of A.file 1 2 3 4 contents of B.file 1 2 3 4 contents of C.file 1 2 3 4 ________________________________ To: Steve Shen <sshen@bu.edu> Cc: Thomas Hampton <thomas.h.hampton@dartmouth.edu>; bioconductor@stat.math.ethz.ch Sent: Wed, June 2, 2010 7:06:34 PM Subject: Re: [BioC] venn diagrams Thanks Steve I used this tutorial: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_graphics_ venn which clearly demonstrates how to use OverLapper. I only wished that all the packages from R and bioconductor could be written with the clarity and simplicity as the tutorial above..... ________________________________ From: Steve Shen <sshen@bu.edu> Cc: Thomas Hampton <thomas.h.hampton@dartmouth.edu>; bioconductor@stat.math.ethz.ch Sent: Wed, June 2, 2010 6:51:04 PM Subject: Re: [BioC] venn diagrams You can try overLapper function in BioC instruction. It will do up to five lists. Steve Thanks Thomas > >>can you or someone give me a clue on how to load the files and then generate a venn diagram and the various data sets that lists the union/intesect/unique members. I have read the gplots but its not clear to me as a newbie. > > > > > > >>----- Original Message ---- >>From: Thomas Hampton <thomas.h.hampton@dartmouth.edu> >>Cc: bioconductor@stat.math.ethz.ch >>Sent: Wed, June 2, 2010 4:03:07 PM >>Subject: Re: [BioC] venn diagrams > >>You might try gplots: > >>venn package:gplots R Documentation > >>Plot a Venn diagram > >>Description: > >> Plot Venn diagrams for up to 5 sets > >>Usage: > >> venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE, >> simplify=FALSE, show.plot=TRUE) > >>best, > >>Tom > >>On Jun 2, 2010, at 3:48 PM, David Lyon wrote: > >>> Sorry newbie question. >>> >>> If I had 6 files named 1,2,3,4 each file containing a ID eg: >>> >>> ENST00000326632 >>> etc. >>> >>> Can someone provide the code that loads each file and generates a Venn Diagram displaying the intersection/unique/union of the data sets in both a table format and a diagramatic format like a jpeg ? >>> >>> Thanks in advance. > >> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>_______________________________________________ >>Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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On 06/05/2010 06:45 PM, David Lyon wrote: > Does anyone know the answer to this simple question > library(gplots) > > This works great from the console: > A <- c(1,2,3,4) > B <- c(1,2,3,4) > C <- c(1,2,3,4) > input<-list(A,B,C) > venn(input) > > When I input the data from flat files each containing in a single col it is only using the first row from each file in the venn diagram > eg: > A <- ("A.file") > B <- ("B.file") > C <- ("C.file") > input<-list(A,B,C) > venn(input) > > its returns the venn diagram from only the first row from each file , how do I change the code so it uses every data point in each column. Hello, the input (?data? in the ?venn man page) should be a named list of _vectors_ . If it is something else, try converting it, maybe like as.vector? I am not familiar with your syntax to read in files. > a<-("b") > a [1] "b" Maybe something like read.table or so is what you really want? Just guessing Steffen
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Thanks for your efforts Steffen. If anyone knows exactly how to get this working I would be appreciative: eg: library(gplots) A <- read.delim ("A.file") B <- read.delim ("B.file") C <- read.delim ("C.file") input<-list(A,B,C) venn(input) its returns the venn diagram from only the first row from each file , how do I change the code so it uses every data point in each column. Thanks contents of A.file 1 2 3 4 contents of B.file 1 2 3 4 contents of C.file 1 2 3 4
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Your have to turn your sets into vectors objects first. You could do this in one step with readLines A <- readLines("A.file") or after read.delim() you would convert the resulting data frames to vectors like this: A <- read.delim ("A.file") A <- as.character(as.matrix(A)) Thomas On Sat, Jun 05, 2010 at 11:50:34AM -0700, David Lyon wrote: > Thanks for your efforts Steffen. > > If anyone knows exactly how to get this working I would be appreciative: > > > > > eg: > library(gplots) > A <- read.delim ("A.file") > B <- read.delim ("B.file") > C <- read.delim ("C.file") > input<-list(A,B,C) > venn(input) > > its returns the venn > diagram from only the first row from each file , how do I change the > code so it uses every data point in each column. > > > Thanks > > > > contents > of A.file > 1 > 2 > 3 > 4 > > contents of B.file > 1 > 2 > 3 > 4 > > contents of C.file > 1 > 2 > 3 > 4 > > > > > _______________________________________________ > 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 >
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Thank you very much that works. Cheers! ----- Original Message ---- From: Thomas Girke <thomas.girke@ucr.edu> To: David Lyon <david_lyon3 at="" yahoo.com=""> Cc: Steffen M?ller <steffen_moeller at="" gmx.de="">; bioconductor at stat.math.ethz.ch Sent: Sat, June 5, 2010 3:15:45 PM Subject: Re: [BioC] venn diagrams Your have to turn your sets into vectors objects first. You could do this in one step with readLines A <- readLines("A.file") or after read.delim() you would convert the resulting data frames to vectors like this: A <- read.delim ("A.file") A <- as.character(as.matrix(A)) Thomas On Sat, Jun 05, 2010 at 11:50:34AM -0700, David Lyon wrote: > Thanks for your efforts Steffen. > > If anyone knows exactly how to get this working I would be appreciative: > > > > > eg: > library(gplots) > A <- read.delim ("A.file") > B <- read.delim ("B.file") > C <- read.delim ("C.file") > input<-list(A,B,C) > venn(input) > > its returns the venn > diagram from only the first row from each file , how do I change the > code so it uses every data point in each column. > > > Thanks > > > > contents > of A.file > 1 > 2 > 3 > 4 > > contents of B.file > 1 > 2 > 3 > 4 > > contents of C.file > 1 > 2 > 3 > 4 > > > > > _______________________________________________ > 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 >
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Hi Thomas, the "as.matrix" did the trick. The challenge is to lose the "data.frame", which I find somewhat counter-intuitive at times: # creating some data frome > a<-data.frame(1:3,4:6) > a X1.3 X4.6 1 1 4 2 2 5 3 3 6 > dim(a) [1] 3 2 # Instruction to lose the dimension > dim(a)<-NULL # no warning no nothing, the data.format is kept > dim(a) [1] 3 2 # The same as a matrix just works > a<-as.matrix(a) > dim(a) [1] 3 2 > dim(a)<-NULL > a [1] 1 2 3 4 5 6 This is all understandable, I nonetheless hope to find where getVennCounts is affected by this or something else data.frame-specific. It should at least stop() if it does not work with data.frames. Best, Steffen On 06/05/2010 09:15 PM, Thomas Girke wrote: > Your have to turn your sets into vectors objects first. You > could do this in one step with readLines > > A <- readLines("A.file") > > or after read.delim() you would convert the resulting data frames to > vectors like this: > > A <- read.delim ("A.file") > A <- as.character(as.matrix(A)) > > Thomas > > On Sat, Jun 05, 2010 at 11:50:34AM -0700, David Lyon wrote: >> Thanks for your efforts Steffen. >> >> If anyone knows exactly how to get this working I would be appreciative: >> >> >> >> >> eg: >> library(gplots) >> A <- read.delim ("A.file") >> B <- read.delim ("B.file") >> C <- read.delim ("C.file") >> input<-list(A,B,C) >> venn(input) >> >> its returns the venn >> diagram from only the first row from each file , how do I change the >> code so it uses every data point in each column. >> >> >> Thanks >> >> >> >> contents >> of A.file >> 1 >> 2 >> 3 >> 4 >> >> contents of B.file >> 1 >> 2 >> 3 >> 4 >> >> contents of C.file >> 1 >> 2 >> 3 >> 4 >> >> >> >> >> _______________________________________________ >> 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 >>
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Hello again, David. I can confirm your problem (or at least that there is something strange). What repairs it for me is venn(list(a[,1],b[,1],c[,1])) which does what I had previously hoped the "as.vector" to achieve. I'm having a close look at that and send a patch. Cheers, Steffen On 06/05/2010 08:50 PM, David Lyon wrote: > Thanks for your efforts Steffen. > > If anyone knows exactly how to get this working I would be appreciative: > > > > > eg: > library(gplots) > A <- read.delim ("A.file") > B <- read.delim ("B.file") > C <- read.delim ("C.file") > input<-list(A,B,C) > venn(input) > > its returns the venn > diagram from only the first row from each file , how do I change the > code so it uses every data point in each column. > > > Thanks > > > > contents > of A.file > 1 > 2 > 3 > 4 > > contents of B.file > 1 > 2 > 3 > 4 > > contents of C.file > 1 > 2 > 3 > 4 > > >
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