How to work on MCC trees annotations

[Mj]

Dear Marc and dear all,

I have performed BEAST v1.8.2 phylogeographic analysis (RWW continuous diffusion models) and extracted maximum clade credibility trees using Tree Annotator.

I wanted to work on annotations of trees thanks to the read.annotated.nexus function of the OutbreakTools package. However, when I plot the tree in R in it is not the same I obtained using FigTree v1.4.2. The topology looks similar but taxa are not distributed on the same way.

I can’t understand why. Here is the simple R code I am using:
library(OutbreakTools)
tree <- read.annotated.nexus(“MCC_Tree.tree")
plot(tree, cex=0.2, font=1, family=“Arial")

Could you please help me? Can I work on annotations in R even if it seems to have a problem? .. or is there another way to work properly on branchs' and nodes' annotations (diffusion rates, latitudes and longitudes of internal nodes...)?

Any thoughts would be appreciated.

Here attached the trees I obtained with both softwares and the nexus file.

Many thanks,

Maude

[Marc Suchard]

Hi Maude,

I recently (May 2015) made some significant fixes to read.annotated.nexus() and am not sure if Thibaut has updated the OutbreakTools version on CRAN.  So, please try to install the development version (instructions below) and see if that fixes your issue.  If you are still having trouble with the development version, please let me know and I try to schedule some time to take a closer look at your *.tree file.

To install the development version of OutbreakTools

  

  install.packages("devtools")

  devtools::install_github("thibautjombart/OutbreakTools")

Finally, Thibaut continues to put a large amount of effort into OutbreakTools, so please remember to cite: Jombart et al. (2014) Epidemics, 7, 28 - 34.

best, Marc

[Mj]

Hi Marc,

I looks much better. Thank you very much.

Of course, I'll let you know if I can see anything else.

Best wishes,

Maude

[Maude Jacquot]

Hi again Marc,

Is there any way to read multiple annotated trees on the same time? I mean, if I want to work on the .trees files generated by BEAST (phylogeography) and which contain all the sampled annotated-trees along the MCMC.
All I tried did not work.

Thanks,

Maude

[Marc A. Suchard]

Hi Maude,

It looks like I need to update the multi-tree reading capability in OutbreakTools. Can you email me an example *.tre file with multiple trees that you’d like to be able to load?

best, Marc

[Maude Jacquot]

Hi Marc,

Thank you for your reply. Here, is the example on which I am working to perform tests (113 Taxa, 4 annotated trees).

Many thanks for your help,

Maude

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Maude JACQUOT
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary & Life Sciences
Room 306, Graham Kerr Building
University of Glasgow, Glasgow, G12 8QQ
Tél: +44 (0)141 330 6626

[Marc Suchard]

I committed a bug-patch to OutbreakTools this morning and think I am able to correct read those 4 trees.  Try:

    devtools::install_github("thibautjombart/OutbreakTools")

    trees <- read.annotated.nexus("MultiAnnotated_test.trees")

best, Marc

[Maude Jacquot]

Hi Marc,

I re-installed and loaded the development version of OutbreakTools.
>  devtools::install_github("thibautjombart/OutbreakTools")
> library(OutbreakTools)

Now, I can read the 4 trees,
> Trees <- read.annotated.nexus("MultiAnnotated_test.trees")
> Trees
4 phylogenetic trees

But I still have problem to access to the annotations. I only get tip labels:
> names(Trees[1]$annotations)
[1] "tip.label"
> names(Trees[1]$annotations[[1]])
NULL

For each tree, I would like to get the whole annotations such as:
> Tree <- read.annotated.nexus("SingleTree_test.tree")>
> names(Tree$annotations[[1]])
 [1] "location.rate"            "length_range"               
 [3] "location2_median"         "height_range"               
 [5] "location1_range"          "rate_95%_HPD"               
 [7] "location.rate_range"      "rate_range"                 
 [9] "location2_80%HPD_1"       "location1_80%HPD_1"     
[11] "rate"                         "height"                     
[13] "rate_median"                  "length"                     
[15] "location1_median"         "height_95%_HPD"             
[17] "length_95%_HPD"               "location.rate_median"   
[19] "height_median"                "location2_range"        
[21] "posterior"                    "location_80%HPD_modality"
[23] "location2"                "location1"              
[25] "length_median"                "location.rate_95%_HPD"  

Maybe I'm doing something wrong. Sorry about that and many thanks for your prompt answers, I really appreciate it!

Best wishes,

Maude

[Bram]

Hi Maude,

To acces an annotation 'X', you can follow the instructions (on p41) of the outbreaktools manual:
annotX <- unlist(sapply(tree$annotations, function(e) e$X))
or access them directly
tree$annotations[[traitIndex]][traitName][[1]][1]

Good luck,
Bram


Op maandag 10 augustus 2015 17:32:39 UTC+2 schreef Maude Jacquot:

[Marc Suchard]

Hi Maude,

Am not sure what to suggest here.   I get the following in a fresh R environment:

> devtools::install_github("thibautjombart/OutbreakTools")

Downloading github repo thibautjombart/OutbreakTools@master

Installing OutbreakTools

'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \

  '/private/var/folders/hj/cd3d04l17yx9698r3mw0zhzm0000gn/T/Rtmpq8aMQ2/devtools131961073a4d/thibautjombart-OutbreakTools-5bf5380'  \

  --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' --install-tests 

* installing *source* package ‘OutbreakTools’ ...

** R

** data

** inst

** preparing package for lazy loading

Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘OutbreakTools’

Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘OutbreakTools’

Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘OutbreakTools’

Creating a generic function for ‘summary’ from package ‘base’ in package ‘OutbreakTools’

Creating a generic function for ‘head’ from package ‘utils’ in package ‘OutbreakTools’

Creating a generic function for ‘tail’ from package ‘utils’ in package ‘OutbreakTools’

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (OutbreakTools)

> library(OutbreakTools)

Loading required package: ggplot2

Loading required package: network

network: Classes for Relational Data

Version 1.10.2 created on 2014-06-12.

copyright (c) 2005, Carter T. Butts, University of California-Irvine

                    Mark S. Handcock, University of California -- Los Angeles

                    David R. Hunter, Penn State University

                    Martina Morris, University of Washington

                    Skye Bender-deMoll, University of Washington

 For citation information, type citation("network").

 Type help("network-package") to get started.

Loading required package: knitr

 OutbreakTools 0.1-13.999 has been loaded

> Trees <- read.annotated.nexus("MultiAnnotated_test.trees")

> names(Trees[[1]]$annotations[[1]])

[1] "locationSeg1.rate" "locationSeg1"      "rate" 

and these appear to be the only traits that I see MultiAnnotated_test.trees.  

best, M

[Santiago Sánchez]

From what I see, I think Maude missed two square brackets (highlighted in red) in her example:

> names(Trees[[1]]$annotations[[1]])

Cheers,

Santiago

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Santiago Sánchez-Ramírez

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[Maude Jacquot]

Dear all,

Santiago has seen right: missing brackets, sorry. Now, I am glad to be able to work on multi-annotated tree!
Your help was definitively very useful. Many thanks.

All the best,

Maude