findGroves
(Package: treescape) :
Identify clusters of similar trees
This function uses hierarchical clustering on principal components output by treescape to identify groups of similar trees. Clustering relies on hclust, using Ward's method by default.
● Data Source:
CranContrib
● Keywords:
● Alias: findGroves
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Function to make the most recent common ancestor (MRCA) matrix of a tree, where entry (i,j) gives the MRCA of tips i and j. The function is linear, exploiting the fact that the tree is rooted.
● Data Source:
CranContrib
● Keywords:
● Alias: linearMrca
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tipDiff
(Package: treescape) :
Find tip position differences
Find the topologicial differences between two trees with the same tip labels. The function returns a data frame of the tips and the number of differences in their ancestry between the two trees. Called by plotTreeDiff, which highlights the differing tips in a plot of the two trees.
● Data Source:
CranContrib
● Keywords:
● Alias: tipDiff
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treeVec
(Package: treescape) :
Tree vector function
Function which takes an object of class phylo and outputs the vector for the Kendall Colijn metric. The elements of the vector are numeric if return.lambda.function=FALSE (default), and otherwise they are functions of lambda.
● Data Source:
CranContrib
● Keywords:
● Alias: treeVec
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Comparison of two trees using the Kendall Colijn metric
● Data Source:
CranContrib
● Keywords:
● Alias: treeDist
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This function opens up an application in a web browser for an interactive exploration of the diversity in a set of trees. For further details please see the "help" tab within the application.
● Data Source:
CranContrib
● Keywords:
● Alias: treescapeServer
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plotGrovesD3
(Package: treescape) :
Scatterplot of groups of trees using code{scatterD3
This function displays the scatterplot of the Multidimensional Scaling (MDS) output by treescape, superimposing group information (derived by findGroves) using colors. scatterD3 enables interactive plotting based on d3.js, including zooming, panning and fading effects in the legend.
● Data Source:
CranContrib
● Keywords:
● Alias: plotGrovesD3
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refTreeDist
(Package: treescape) :
Metric function for comparing a reference code{phylo
Comparison of a single reference tree to a list of trees using the Kendall Colijn metric. Output is given as a vector of distances from the reference tree.
● Data Source:
CranContrib
● Keywords:
● Alias: refTreeDist
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Highlight the topologicial differences between two trees, plotted side by side. This function is useful for comparing representative "median" trees - see medTree. It relies on the function tipDiff.
● Data Source:
CranContrib
● Keywords:
● Alias: plotTreeDiff
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treescape
(Package: treescape) :
Phylogenetic tree exploration
Compares phylogenetic trees and maps them into a small number of dimensions for easy visualisation and identification of clusters.
● Data Source:
CranContrib
● Keywords:
● Alias: treescape
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