Re: [R-sig-phylo] circle plot
Shota Nakamura said -- > Following Luke's advise, I edited fan tree by Illustrator. > I got the image I want. > > Please find attached. > Left image is output of "ape", right one is edited version. > > If you have an idea to do this by "ape", tell me please. This is an illegitimate answer, but ... have APE call PHYLIP's program Drawgram. It can do a Circular tree, and by playing around with the options for use or nonuse of branch lengths, and the placement of ancestral nodes, you can get the circular tournament-format tree. Joe Joe Felsenstein [EMAIL PROTECTED] Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] circle plot
Great ! I got that image by R. Manys thanks for your kind help !! Shota >> Following Luke's advise, I edited fan tree by Illustrator. >> I got the image I want. >> >> Please find attached. >> Left image is output of "ape", right one is edited version. >> >> If you have an idea to do this by "ape", tell me please. >> Thank you very much for your help. > > You could use compute.brlen() with the default "Grafen" method. Then > you tune the "power" parameter so it suits your needs. For instance, > with a random 1000-tip tree: > > plot(compute.brlen(tr, power = 0.5), "f") > > Of course, you have to leave the default use.edge.length = TRUE now. > You may also use a function of your own to compute the branch lengths. > > Best, > > EP > >> Shota >> >>> Another solution to this type of problem is to plot your phylogram to >>> a large pdf (for Emmanuel's example, at least 60 x 60 inches), and >>> then edit it in Adobe illustrator. >>> >>> >>> library(ape) >>> >>> pdf(file="test.pdf", width=60, height=60) >>> tr <- rtree(1000) >>> plot(tr, "f", FALSE) >>> dev.off() >> Thank you very much for your prompt response. Actually, I've already tried a radial plot. The tree I want to make is like radial plot as tournament format. I hope this reply makes sense. >>> >>> Not to me. Can you send a picture with this format? >>> >>> EP >>> Sorry for poor explanation. Shota >> Dear all, >> >> I would like to make a circle plot by the ape package. >> >> I tried to make it by the command "plot.phylo(bigtree, >> use.edge.length = >> FALSE, type = fan)". >> But big tree make it hard to see. > > Indeed, if I do this: > > tr <- rtree(1000) > plot(tr, "f", FALSE) > > I have a nice artistic picture, but not a readable tree. > > Have you tried type = "radial", or plot(tr, "r")? Alternatively, > type="f" with the default use.edge.length = TRUE and show.tip.label > = FALSE shows more clearly the tree topology. > >> The image I want is like circle plot (topology only) of MEGA4. >> And keeping complete circle is needed. > > I don't know what MEGA does, but this seems to be close to type = > "radial". > > HTH > > EP > >> Does anyone have a good idea (edit function or source) for making >> it? >> Please give me your advise. >> Thanks, >> >> Shota Nakamura >> Genome Information Research Center, Osaka University >> >> ___ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] circle plot
Shota Nakamura <[EMAIL PROTECTED]> a écrit : Following Luke's advise, I edited fan tree by Illustrator. I got the image I want. Please find attached. Left image is output of "ape", right one is edited version. If you have an idea to do this by "ape", tell me please. Thank you very much for your help. You could use compute.brlen() with the default "Grafen" method. Then you tune the "power" parameter so it suits your needs. For instance, with a random 1000-tip tree: plot(compute.brlen(tr, power = 0.5), "f") Of course, you have to leave the default use.edge.length = TRUE now. You may also use a function of your own to compute the branch lengths. Best, EP Shota Another solution to this type of problem is to plot your phylogram to a large pdf (for Emmanuel's example, at least 60 x 60 inches), and then edit it in Adobe illustrator. library(ape) pdf(file="test.pdf", width=60, height=60) tr <- rtree(1000) plot(tr, "f", FALSE) dev.off() Thank you very much for your prompt response. Actually, I've already tried a radial plot. The tree I want to make is like radial plot as tournament format. I hope this reply makes sense. Not to me. Can you send a picture with this format? EP Sorry for poor explanation. Shota Dear all, I would like to make a circle plot by the ape package. I tried to make it by the command "plot.phylo(bigtree, use.edge.length = FALSE, type = fan)". But big tree make it hard to see. Indeed, if I do this: tr <- rtree(1000) plot(tr, "f", FALSE) I have a nice artistic picture, but not a readable tree. Have you tried type = "radial", or plot(tr, "r")? Alternatively, type="f" with the default use.edge.length = TRUE and show.tip.label = FALSE shows more clearly the tree topology. The image I want is like circle plot (topology only) of MEGA4. And keeping complete circle is needed. I don't know what MEGA does, but this seems to be close to type = "radial". HTH EP Does anyone have a good idea (edit function or source) for making it? Please give me your advise. Thanks, Shota Nakamura Genome Information Research Center, Osaka University ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] circle plot
Shota Nakamura <[EMAIL PROTECTED]> a écrit : Thank you very much for your prompt response. Actually, I've already tried a radial plot. The tree I want to make is like radial plot as tournament format. I hope this reply makes sense. Not to me. Can you send a picture with this format? EP Sorry for poor explanation. Shota Dear all, I would like to make a circle plot by the ape package. I tried to make it by the command "plot.phylo(bigtree, use.edge.length = FALSE, type = fan)". But big tree make it hard to see. Indeed, if I do this: tr <- rtree(1000) plot(tr, "f", FALSE) I have a nice artistic picture, but not a readable tree. Have you tried type = "radial", or plot(tr, "r")? Alternatively, type="f" with the default use.edge.length = TRUE and show.tip.label = FALSE shows more clearly the tree topology. The image I want is like circle plot (topology only) of MEGA4. And keeping complete circle is needed. I don't know what MEGA does, but this seems to be close to type = "radial". HTH EP Does anyone have a good idea (edit function or source) for making it? Please give me your advise. Thanks, Shota Nakamura Genome Information Research Center, Osaka University ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] circle plot
Another solution to this type of problem is to plot your phylogram to a large pdf (for Emmanuel's example, at least 60 x 60 inches), and then edit it in Adobe illustrator. library(ape) pdf(file="test.pdf", width=60, height=60) tr <- rtree(1000) plot(tr, "f", FALSE) dev.off() On Nov 12, 2008, at 7:29 AM, Emmanuel Paradis wrote: > Shota Nakamura <[EMAIL PROTECTED]> a écrit : >> Dear all, >> >> I would like to make a circle plot by the ape package. >> >> I tried to make it by the command "plot.phylo(bigtree, >> use.edge.length = >> FALSE, type = fan)". >> But big tree make it hard to see. > > Indeed, if I do this: > > tr <- rtree(1000) > plot(tr, "f", FALSE) > > I have a nice artistic picture, but not a readable tree. > > Have you tried type = "radial", or plot(tr, "r")? Alternatively, > type="f" with the default use.edge.length = TRUE and show.tip.label > = FALSE shows more clearly the tree topology. > >> The image I want is like circle plot (topology only) of MEGA4. >> And keeping complete circle is needed. > > I don't know what MEGA does, but this seems to be close to type = > "radial". > > HTH > > EP > >> Does anyone have a good idea (edit function or source) for making it? >> Please give me your advise. >> Thanks, >> >> Shota Nakamura >> Genome Information Research Center, Osaka University >> >> ___ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] circle plot
Thank you very much for your prompt response. Actually, I've already tried a radial plot. The tree I want to make is like radial plot as tournament format. I hope this reply makes sense. Sorry for poor explanation. Shota Dear all, I would like to make a circle plot by the ape package. I tried to make it by the command "plot.phylo(bigtree, use.edge.length = FALSE, type = fan)". But big tree make it hard to see. Indeed, if I do this: tr <- rtree(1000) plot(tr, "f", FALSE) I have a nice artistic picture, but not a readable tree. Have you tried type = "radial", or plot(tr, "r")? Alternatively, type="f" with the default use.edge.length = TRUE and show.tip.label = FALSE shows more clearly the tree topology. The image I want is like circle plot (topology only) of MEGA4. And keeping complete circle is needed. I don't know what MEGA does, but this seems to be close to type = "radial". HTH EP Does anyone have a good idea (edit function or source) for making it? Please give me your advise. Thanks, Shota Nakamura Genome Information Research Center, Osaka University ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] circle plot
Shota Nakamura <[EMAIL PROTECTED]> a écrit : Dear all, I would like to make a circle plot by the ape package. I tried to make it by the command "plot.phylo(bigtree, use.edge.length = FALSE, type = fan)". But big tree make it hard to see. Indeed, if I do this: tr <- rtree(1000) plot(tr, "f", FALSE) I have a nice artistic picture, but not a readable tree. Have you tried type = "radial", or plot(tr, "r")? Alternatively, type="f" with the default use.edge.length = TRUE and show.tip.label = FALSE shows more clearly the tree topology. The image I want is like circle plot (topology only) of MEGA4. And keeping complete circle is needed. I don't know what MEGA does, but this seems to be close to type = "radial". HTH EP Does anyone have a good idea (edit function or source) for making it? Please give me your advise. Thanks, Shota Nakamura Genome Information Research Center, Osaka University ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
