perform_MDS: Classical MDS of six difference tree distances Performs...

In svteichman/TreeVizPackage: Tree Visualization Package

Classical MDS of six difference tree distances Performs Classical MDS for a set of trees using six different distances. Add names and references later.

Description

Classical MDS of six difference tree distances Performs Classical MDS for a set of trees using six different distances. Add names and references later.

Usage

perform_MDS(trees, tree_names = NULL, consensus = NULL)

Arguments

trees	A list of phylogenetic trees. If list includes a consensus tree, it should be the first tree.
tree_names	An optional list of gene names to add to the dataframes.
consensus	An optional argument specifying whether the first tree is a consensus tree, and if so the name of the consensus tree.

Value

A list containing two dataframes. The first, of dimension 2 \cdot (n_tree\cdot n_dist), contains the first two MDS coordinates for each tree and distance combination. The second, of dimension (n_tree -1)\cdot n_dist contains the distances from the first tree to each of the other trees for each distance.

svteichman/TreeVizPackage documentation built on June 22, 2022, 11:21 p.m.