[statistical exploration of landscapes of phylogenetic trees]
treescape implements statistical tools for the exploration of
sets of phylogenetic trees describing the evolutionary relationships between the same taxa.
This web interface provies an easy access to the resoures implemented in the package.
The tree landscape explorer is made of two panels: a sidebar used to define inputs and various
customizations, and a main analysis panel displaying results.
The main panel displays two types of outputs:
- the scatterplot of a Metric Multidimensional Scaling
(MDS, a.k.a. Principal Coordinates Analysis, PCoA), providing the best reduced-spaced visualisation
of the distances between trees
- an optional plot of a specific tree; a valid tree label or number needs to be provided.
The sidebar contains the following sections:
- Input/output: to choose the analysed dataset
and export data and results to various files
- Analysis: to customize the analysis
- Aesthetics: to customize graphics
Input/output
treescape needs a list of phylogenetics trees as input.
Input
The user can choose between data distributed with the package, or provide input files.
Two types of input files can be used:
- R objects saved using the function save(x, file="x.RData")
where 'x' is a list of trees of the class multiphylo (from the ape package. Accepted extensions are ".RData" and ".rda".
- list of trees saved in a nexus file, e.g. using ape's function write.nexus(x, file="x.nex") in R.
Output
Trees and analysis results can be exported to various formats.
Currently available options are:
- saving trees to a Nexus file (.nex)
- saving results as .csv file (spreadsheet-like text file; compatible with most systems);
results are output as a table where each row is a tree label, and columns contain optional
clustering results as well as principal components (PC) of the Metric Multidimensional Scaling
(MDS) of the tree space
- saving results as an R object (.RData); in this case, two objects will be saved in the
.RData: `trees` will be a list of trees of class `multiPhylo`, and `analysis` will be the results
of the analysis; when clusters are not inferred, `analysis` is the output of the function
`treescape`; when clusters are inferred, `analysis` is the output of the function `findGroves`
Note that to save images, you can right-click/long-click(Mac) on the image to save and select
'save as ...'.
Analysis
Metric
The metric to be used to measure distances between tips of the trees:
- metric: the tree metric developed by Kendall & Colijn; used by default
- patristic: the sum of branch lengths on the shortest path between pairs of tips
(see ?distTips in the package adephylo)
- Number of nodes: the total number of internal nodes on the shortest path between pairs of tips
(see ?distTips in the package adephylo)
- Abouheif: the Abouheif metric
(see ?distTips in the package adephylo)
- Sum of direct descendents: another metric related to the Abouheif metric
(see ?distTips in the package adephylo)
Lambda
The value of lambda used in Kendall & Colijn's metric.
Number of MDS axes retained
The number of principal components to retain in the Metric Multidimensional Scaling (MDS).
x/y axes
Used to select which principal components are represented as x and y axes on the scatterplot.
Aesthetics
A number of graphical options are available. If a tree is plotted on the main panel, then a number
of new options will be available (scroll down to access them).
More information
treescape is developed on github.
For questions, bug reports, feature requests and contributions, please
use github's issue system.
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