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
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
> 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 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
>>
>>
>>
>>
>> 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
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>> 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*
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