Hello, I used the code insertion that Emmanuel provided, and that solved my issue. Thank you all for the help and discussion!
Pascal, if you're looking for a tutorial, this is the first one I found when I started: http://www.phytools.org/eqg/Exercise_3.2/ I've found it *very* helpful. I've also worked through this one, which uses ggtree like you're looking into: https://4va.github.io/biodatasci/r-ggtree.html For specifics, it would help if you came up with a minimum reproducible example <https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example> and shared it (especially code!). You might get a better response from people. Cheers On Sat, Aug 25, 2018 at 11:53 PM, pascal de Clarens <pdeclar...@gmail.com> wrote: > Hello, > > I am using Iramuteq with ape and get the trees with iriba method > I have not yet understand how to make a phylogenic tree ... is there a > tutorail available? > > I installed the ggtree package, but when I try to use the Reinert > classification method I gnow get this message: > > None > > Warning message: > > package ‘Matrix’ was built under R version 3.4.4 > > There were 42 warnings (use warnings() to see them) > > There were 25 warnings (use warnings() to see them) > > Warning message: > > package ‘ape’ was built under R version 3.4.4 > > Error in Ntip + Nnode : non-numeric argument to binary operator > > Calls: plot.dendropr -> plot.phylo > > Execution halted > > > thanks for your help > > > best regards > > Le ven. 24 août 2018 à 17:59, Bjørn Tore Kopperud <b.t.koppe...@nhm.uio.no> > a écrit : > >> Hi Nick, >> >> >> There is a fantastic package for visualizing trees, the "ggtree" package: >> >> >> https://github.com/GuangchuangYu/ggtree >> >> >> Here is a vignette with several examples on how to display trees, >> including your circular phylogram visualization: >> >> >> https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ >> treeVisualization.html#phylogram-and-cladogram >> >> >> You can read the documentation to figure out how to plot tip labels, I'm >> sure it's possible. The ggtree package is very powerful but also different >> in comparison with ape, as it is built on top of the "grammar of graphics" >> ggplot package. >> >> >> Best, >> >> Bjørn Tore Kopperud >> >> >> G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for >> visualization and annotation of phylogenetic trees with their covariates >> and other associated data. *Methods in Ecology and Evolution*. 2017, >> 8(1):28-36. >> >> >> >> ------------------------------ >> *From:* R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of >> Carleson, Nick <carle...@oregonstate.edu> >> *Sent:* 24 August 2018 17:04 >> *To:* email@example.com >> *Subject:* [R-sig-phylo] Aligning tree tip labels together in ape >> >> Hello all, >> >> I'm using the R package 'ape' to make non-ultrametric phylogenetic trees >> . I want to align tip labels together when drawing a tree with >> plot.phylo(), and also add on more labels using the tiplabels() >> function. But, I can't get additional tip labels from tiplabels aligned >> properly with those from plot.phylo. When I call tiplabels, the labels >> are being drawn at the true edge length instead of neatly around the plot >> with the tip labels drawn by plot.phylo. So, in the plot below, I want >> the tip labels (circles) to be aligned adjacent to the tip labels (names) >> drawn by plot.phylo. >> >> Good: tips like t30, t31, and t2 >> Bad: tips like t1, t20, and t21 >> >> >> >> >> Can anyone help me out? >> >> Below is the code to produce the tree above. I'm using ape version 5.1 >> and R version 3.4.3. >> >> library(ape) >> set.seed(31) >> sim_tree <- rlineage(0.1, 0.05) >> plot.phylo(sim_tree, type = "fan", align.tip.label = TRUE) >> tiplabels(pch = 19, col = rainbow(3), offset = 6) >> >> Thanks all! >> >> >> *Nick Carleson * >> >> PhD Student >> * | Oregon State University *Graduate Research Assistant | *Botany and >> Plant Pathology* >> _______________________________________________ >> R-sig-phylo mailing list - Rfirstname.lastname@example.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> > > > -- > Pascal de Clarens > 06 07 85 22 54 > -- *Nick Carleson* PhD Student * | Oregon State University *Graduate Research Assistant | *Botany and Plant Pathology* [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - Remail@example.com https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://firstname.lastname@example.org/