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
