Whoops! nevermind. It appears read.beast was being masked from read.beast in
phyloch. Working now.
Jake
> On Dec 11, 2015, at 12:56 PM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com>
> wrote:
>
> 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
> <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
>> <mailto: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
>>
>> <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:
>>>
>>> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> 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/
>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Subject: Digest Footer
>>>
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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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