There appears to be some issues with ggtree plotting BEAST output - I just
tried to run through the example and got the following errors:
source("https://bioconductor.org/biocLite.R";)
biocLite("ggtree")
require("ggtree")
> file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
> beast <- read.beast(file)
> beast
Phylogenetic tree with 15 tips and 14 internal nodes.
Tip labels:
A_1995, B_1996, C_1995, D_1987, E_1996, F_1997, ...
Rooted; includes branch lengths.
> str(beast)
List of 23
$ edge : int [1:28, 1:2] 16 17 18 18 17 16 19 19 20 20 ...
$ edge.length : num [1:28] 3.1 25.44 9.39 6.39 8.82 ...
$ Nnode : int 14
$ tip.label : chr [1:15] "A_1995" "B_1996" "C_1995" "D_1987" ...
$ rate_range_MIN : num [1:14] NA 0.00137 0.00184 0.00119 0.00135 ...
$ rate_range_MAX : num [1:14] NA 0.00502 0.00422 0.00639 0.00481 ...
$ length_range_MIN : num [1:14] NA 0.00603 15.72468 0.42344 0.46641 ...
$ length_range_MAX : num [1:14] NA 7.71 36.72 11 3.95 ...
$ length_95%_HPD_MIN: num [1:14] NA 0.306 22.049 1.88 1.125 ...
$ length_95%_HPD_MAX: num [1:14] NA 5.18 30.12 6.67 2.93 ...
$ height : num [1:14] 38.04 34.89 9.47 33.62 31.6 ...
$ rate : num [1:14] NA 0.00292 0.00291 0.00291 0.00289 ...
$ rate_median : num [1:14] NA 0.00291 0.0029 0.0029 0.00288 ...
$ length : num [1:14] 0 3.01 25.72 4.35 2.02 ...
$ length_median : num [1:14] NA 3.01 25.58 4.28 2.01 ...
$ rate_95%_HPD_MIN : num [1:14] NA 0.00231 0.00237 0.00228 0.00226 ...
$ rate_95%_HPD_MAX : num [1:14] NA 0.00359 0.00348 0.00357 0.0035 ...
$ height_95%_HPD_MIN: num [1:14] 35.31 31.42 7.32 33.07 30.72 ...
$ height_95%_HPD_MAX: num [1:14] 40.8 38.7 11.6 34.3 32.6 ...
$ height_range_MIN : num [1:14] 33.97 29.2 5.94 33 30.32 ...
$ height_range_MAX : num [1:14] 46.9 42.9 15.1 35.4 33.5 ...
$ height_median : num [1:14] 37.93 34.82 9.39 33.57 31.56 ...
$ posterior : num [1:14] 1 0.941 1 1 1 ...
- attr(*, "class")= chr "phylo"
- attr(*, "origin")= chr
"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/ggtree/extdata/BEAST/beast_mcc.tree"
> plot(beast, annotation="length_0.95_HPD", branch.length="none") + theme_tree()
NULL
Warning messages:
1: In plot.window(...) : "annotation" is not a graphical parameter
2: In plot.window(...) : "branch.length" is not a graphical parameter
3: In plot.xy(xy, type, ...) : "annotation" is not a graphical parameter
4: In plot.xy(xy, type, ...) :
"branch.length" is not a graphical parameter
5: In title(...) : "annotation" is not a graphical parameter
6: In title(...) : "branch.length" is not a graphical parameter
So, there is some issue with plotting, and read.beast is also not parsing all
of the data from internal branches. you can see that it reads data from 14
branches (I think these are the terminal branches?) but there are actually 28
total branches in the example. It would be awesome if this actually could
replace the read.annotated.nexus from OutbreakTools, as this kind of output is
much easier to workwith.
Jake
> On Dec 10, 2015, at 7:42 AM, Yu, Guangchuang <g...@connect.hku.hk> wrote:
>
> Dear Roger,
>
> ggtree can parse BEAST output and visualize BEAST statistics, see the
> document:
> http://www.bioconductor.org/packages/3.2/bioc/vignettes/ggtree/inst/doc/ggtree.html#annotating-tree-with-beast-output
>
> Bests,
> Guangchuang
>
>
> On Thu, Dec 10, 2015 at 7:00 PM, <r-sig-phylo-requ...@r-project.org> wrote:
>
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>> Today's Topics:
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>> 1. Re: Plotting sampled-ancestor trees in R (Roger Close)
>> 2. Implementation of Mir et al.'s (2013) tree balance index?
>> (Gabriel Yedid)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 9 Dec 2015 15:50:11 +0000
>> From: Roger Close <roger.cl...@gmail.com>
>> To: David Bapst <dwba...@gmail.com>
>> Cc: R Sig Phylo Listserv <r-sig-phylo@r-project.org>
>> Subject: Re: [R-sig-phylo] Plotting sampled-ancestor trees in R
>> Message-ID:
>> <CAFauv=
>> ubz3yncju8j+jgpxpfop0na4yy_3o7bayd7csxbvf...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Dave, Emmanuel and Joseph,
>>
>> Thanks very much for your suggestions. The output of BEAST, at least, is an
>> ordinary Newick/NEXUS file with ancestors represented as tips on the ends
>> of zero-length branches (see attached).
>>
>> One way to proceed would be to drop the tips that correspond to ancestors
>> and then add them back on using edge labels. However, I see that paleotree
>> designates ancestors using $anag.tips; is there a tool for plotting this
>> type of tree?
>>
>> Cheers,
>> Roger
>>
>>
>>
>> ---
>> Roger Close, Postdoctoral Research Associate
>> Department of Earth Sciences, Oxford University
>> South Parks Road
>> Oxford OX1 3AN
>> United Kingdom
>>
>> On 8 December 2015 at 18:56, David Bapst <dwba...@gmail.com> wrote:
>>
>>> Hi Roger,
>>>
>>> I'm not aware of any existing solution. Could you send around a small
>>> example of the data format of an output sampled ancestor tree from
>>> BEAST or MrBayes? Are they just typical Newick/NEXUS format with
>>> ancestors indicated tipis with zero-length branches or something more
>>> complicated?
>>>
>>> Remarkably I've not looked at the formatting of one, but obviously
>>> plotting SA trees is something the community will need in the near
>>> future.
>>>
>>> Cheers,
>>> -Dave
>>>
>>> On Tue, Dec 8, 2015 at 5:46 AM, Roger Close <roger.cl...@gmail.com>
>> wrote:
>>>> Hi all,
>>>>
>>>> Does anyone know of a way to plot sampled-ancestor trees in R such that
>>>> ancestors lie on branches, rather than being zero-length terminals that
>>>> follow a bifurcation?
>>>>
>>>> Many thanks,
>>>> Roger
>>>>
>>>> ---
>>>> Roger Close, Postdoctoral Research Associate
>>>> Department of Earth Sciences, Oxford University
>>>> South Parks Road
>>>> Oxford OX1 3AN
>>>> United Kingdom
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
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>>>
>>>
>>> --
>>> David W. Bapst, PhD
>>> Adjunct Asst. Professor, Geology and Geol. Eng.
>>> South Dakota School of Mines and Technology
>>> 501 E. St. Joseph
>>> Rapid City, SD 57701
>>>
>>> http://webpages.sdsmt.edu/~dbapst/
>>> http://cran.r-project.org/web/packages/paleotree/index.html
>>>
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>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 10 Dec 2015 15:50:52 +0800
>> From: Gabriel Yedid <gyedi...@gmail.com>
>> To: r-sig-phylo <r-sig-phylo@r-project.org>
>> Subject: [R-sig-phylo] Implementation of Mir et al.'s (2013) tree
>> balance index?
>> Message-ID:
>> <CAD=
>> v+xfxrpyofojk6q_77v22dg1lwc-s248xoj-xzw0sgur...@mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hello all,
>>
>> Is there any R implementation yet of the tree balance metric described in:
>>
>>
>> Mir, Arnau, Francesc Rossell?, and Lidia Rotger. "A new balance index
>> for phylogenetic trees." Mathematical biosciences 241.1 (2013):
>> 125-136.
>>
>>
>> cheers,
>>
>> Gabe
>>
>>
>>
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>
>
>
> --
> --~--~---------~--~----~------------~-------~--~----~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: http://guangchuangyu.github.io
> -~----------~----~----~----~------~----~------~--~---
>
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