Re: [R-sig-phylo] AGY coding
Hi Karla.
Not sure how you have your sequences stored, but if as a string you can do
it yourself:
str <- gsub("C|T", "Y", str);
As for RY vs. AGY, this paper
is very nice. Basically, if you are using them for phylogenetic inference
it may be that recoding destroys the Markovian property of the alignment,
and that may mislead you downstream. A very interesting consideration that
I feel is not widely known.
HTH.
JWB
On Fri, Aug 24, 2018 at 3:36 PM, Karla Shikev wrote:
> Dear all,
>
> Does anyone have a function for AGY coding of nucleotides?
>
> By the way, any thoughts on using RY- vs AGY-coding?
>
> Thanks!
>
> Karla
>
> [[alternative HTML version deleted]]
>
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Re: [R-sig-phylo] Aligning tree tip labels together in ape
Hi Nick. The following is a 'solution' that works with phytools; however, you should keep in mind that you will not generally be able to use a constant offset value if your tip labels vary in length. In that case, you would either have to use a variable offset or figure out the minimum offset required such that the circles fall outside of the taxon labels. library(phytools) par(lty="dotted",fg="black") plotTree(force.ultrametric(sim_tree,"extend"),type="fan",lwd=1) tiplabels(pch = 19, col = rainbow(3), offset = 6) par(lty="solid",fg="transparent") plotTree(sim_tree,type="fan",lwd=1,add=TRUE) par(fg="black") For a more general solution you might offset your taxon labels by a constant amount, or you can use the function strwidth and some basic trigonometry to find the position outside the taxon labels to draw your circles. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org On 8/24/2018 10:04 AM, Carleson, Nick wrote: 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 byplot.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 - 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/ ___ 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/
Re: [R-sig-phylo] Aligning tree tip labels together in ape
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 on behalf of Carleson, Nick Sent: 24 August 2018 17:04 To: r-sig-phylo@r-project.org 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 [cid:ii_jl74vfw93_16568e27b224020e] 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 - 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/
[R-sig-phylo] AGY coding
Dear all, Does anyone have a function for AGY coding of nucleotides? By the way, any thoughts on using RY- vs AGY-coding? Thanks! Karla [[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/
