I think it unlikely that you'll get such specific help here. Try posting on: R-SIG-phylo: R SIG on phylogenetic and comparative methods and analyses instead.
(I also assume you are aware of: https://CRAN.R-project.org/view=Phylogenetics , but I have no idea whether it is helpful). Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, May 5, 2020 at 2:12 PM Charles Lehnen <charlesleh...@gmail.com> wrote: > > I have trying to combine foodweb outputs like the bipartite package's > plotweb() function of bipartiteD3’s bipartite_D3 function with phylogenetic > trees, similar to a tanglegram. Because of the very large size and a high > amount of variability in my dataset, standard tanglegrams turn out very > convoluted, but the plotweb() outputs are still lovely. > > I was able to export tips to manually order the tips of the plotweb() > output to match the order of the phylogenetic tree tips which allowed me to > align tips manually in Inkscape, but this proved extremely time consuming > whenever I made an addition to my dataset. > > require('ape') > > tree1<-read.tree(text="((A,(B,(C,D))),E);") > tree1<-ladderize(tree1, right = FALSE) > > tree2<-read.tree(text="(F,(G,((H,I),(J,K))));") > > is_tip <- tree1$edge[,2] <= length(tree1$tip.label) > ordered_tips <- tree1$edge[is_tip, 2] > tree1tips<-tree1$tip.label[ordered_tips] > > is_tip <- tree2$edge[,2] <= length(tree2$tip.label) > ordered_tips <- tree2$edge[is_tip, 2] > tree2tips<-tree2$tip.label[ordered_tips] > > > I tried to edit the plotweb() script to accept phylo class variables as an > additional argument, but that was evidently beyond my abilities at this > time. > > I also tried combing the outputs using the grid package, we were able to > visually combine outputs next to one another and match the order of the > tips. However, I have not been able to figure out how to actually line up > the tips of the trees to the outputs of plotweb(). This becomes very > evident with my actual, very large dataset > > require('ape') > require('bipartite') > require('ggplotify') > require('cowplot') > require('grid') > > tree1<-read.tree(text="((A,(B,(C,D))),E);") > tree1<-ladderize(tree1, right = FALSE) > > tree2<-read.tree(text="(F,(G,((H,I),(J,K))));") > > bipartite<-cbind(c(0,2,3,2,0,0),c(2,0,2,4,8,0),c(4,3,0,0,5,0),c(0,2,0,0,0,1),c(0,7,2,2,0,0)) > colnames(bipartite)<-c("D","C","B","A","E") > rownames(bipartite)<-c("K","J","I","H","G","F") > bipartite<-as.data.frame(bipartite) > > p12 = as.grob(~cophyloplot(tree1, tree2)) > bipartite = as.data.frame(t(bipartite)) > p3 = as.grob(~plotweb(bipartite, > method = "normal", > empty = "false", > text.rot = "90" > )) > grid.newpage() > grid.draw(p12) > vp = viewport(x = 0.53, y = 0.6, width = 0.6, height = 0.8, angle = -90) > pushViewport(vp) > grid.draw(p3) > > > If anyone could direct me on how to proceed, I would greatly appreciate it! > I have been coming back to this problem for many months now and have not > been to solve it > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
