Thank you very much, I will try that. Regards,
Greg. On Tue, Jun 8, 2021 at 2:06 PM Liam J. Revell <liam.rev...@umb.edu> wrote: > Dear Greg. > > I've never tried this package; however, it's not difficult to either > substitute the set of values that are the branch lengths of a "phylo" > object with a different set of values, or to multiple them by a > different set. > > For example, if you have the set of rates for your trait in a vector > ordered by the edge lengths of the tree, you could just take your > original tree (phy), substitute the edge-specific rates (sig2), then > plot your tree as follows: > > phy.sig2<-phy > phy.sig2$edge.length<-sig2 > phytools::plotTree(phy.sig2) > > Alternatively, if you want to show the amount of evolution that's > expected to occur on each edge, that would be equivalent to the product > of the edge length and it's edge-specific rate. > > phy.sig2<-phy > phy.sig2$edge.length<-phy$edge.length*sig2 > phytools::plotTree(phy.sig2) > > I hope I'm understanding the problem correctly. > > All the best, Liam > > Liam J. Revell > University of Massachusetts Boston [Assoc. Prof.] > Universidad Católica de la Ssma Concepción [Adj. Res.] > > Web & phytools: > http://faculty.umb.edu/liam.revell/, http://www.phytools.org, > http://blog.phytools.org > > On 6/8/2021 4:09 PM, Gregory Mutumi wrote: > > EXTERNAL SENDER > > > > battree.nexus > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1n_sSFcP23nyLiIC49wcEZXUCVWIpOYk1%2Fview%3Fusp%3Ddrive_web&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086523020%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=Hpdeo4rAo8rlRxETrg93gb7aBt47VwXdET6qoDerxPg%3D&reserved=0 > > > > BayesPCM9.Log.txt > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F168ii9utfUlUEqq2LXDy3C9FKe7bCm9w9%2Fview%3Fusp%3Ddrive_web&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=VOXQDIuyPzvzX2p605Z5OG0pxecy%2Bdpj7oaL%2BGFZdQ4%3D&reserved=0 > > > > BayesPCM9.Output.trees > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1th9D4-PMo9f8U9vlHARxFgnxUx8nUPUD%2Fview%3Fusp%3Ddrive_web&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=9PJZV%2FHz26CwsWjoWDVN8THuGe7doTglTix7C5s1fmI%3D&reserved=0 > > > > BayesPCM9.Schedule.txt > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1nhUUcSU6xJrgIeup_sDLABe4WXh6Y3Rf%2Fview%3Fusp%3Ddrive_web&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=LA1nmxEjiWePbyIG1ANTwDNT%2FeGL4qrqtvlOTLh6Vk0%3D&reserved=0 > > > > BayesPCM9.Stones.txt > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1tOcDqbMw840CkErCgiOiuj2Sf0-r_vCl%2Fview%3Fusp%3Ddrive_web&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=DxAe1O2%2FiHoXsxIaF%2BCUT9quQJkTaWutwm9gtA3kZ1M%3D&reserved=0 > > > > BayesPCM9.VarRates.txt > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1wNhBg9QvKj_5RPPE1wK2C1AeiWODEaPL%2Fview%3Fusp%3Ddrive_web&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=7ecLdWeGU1mH0xHdIzzZc57MBCTdsvXOgVOOShX1eMg%3D&reserved=0 > > > > Dear All > > > > Is there a way in BTprocessR or BTRTools (or any other package) to plot a > > tree in such a way that the branch lengths are scaled by rate. Colour > > gradients are a bit difficult to compare across many structures. I am > > looking for a plot where faster rates make branches longer and slower > rates > > produce shorter branches. > > > > The plotshifts function in BTRTools plots the tree with color gradient > > depicting the rates. I am thinking maybe there is an option I am missing > > out that simply does the trick to plot branches scaled by rate? > > > > Please also help me with how to make the legend not plot over the scale. > I > > am not getting how to command the legend positions, I get errors if I try > > the available option, maybe I am missing out something. > > > > My code goes like this: > > > > btresults9 <- rjpp(rjlog = "BayesPCM9.VarRates.txt", rjtrees = > > "BayesPCM9.Output.trees",tree = my.tree, burnin = 0, thinning = 1, > verbose > > = TRUE) > > > > plotShifts(btresults9, plot.options = list(layout = c("e")), tips = T) > > > > I have also attached the files here > > > > Thank you. > > > > Regards, > > > > Greg. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=cnkFpHr39zd9oBaAT9XUCShYVx1LJmSyIvT0v1eirYQ%3D&reserved=0 > > Searchable archive at > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=04%7C01%7Cliam.revell%40umb.edu%7Cfcee1f8fa0eb404382e108d92ab96851%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637587798086533011%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=SFyhGPPDAlfZMDoJokRgAdtDnALDorOAkvl1SEAHv9A%3D&reserved=0 > > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
