Plot.Another.TreeSI: A function to visualize QIRP of additional data across a tree...

In carolinafishes/PhyInformR: Rapid Calculation of Phylogenetic Information Content

Description

A function to visualize QIRP of additional data across a tree topology

Usage

Plot.Another.TreeSI(tree, ratevector, s, color, type)

Arguments

tree	A phylogenetic tree
ratevector	site rate vector, converted to class 'matrix'
s	A number representing the character state space that generated the site rates e.g., s=2 for binary data
color	Color of line e.g., color="blue"
type	plotting function for lines e.g., type=3

Value

A graphical representation of QIRP at every node

Author(s)

A. Dornburg

References

Hwang, J., Jonathan, H., Qi, Z., Yang, Z. L., Zheng, W., and Townsend, J. P. “Solving the Ecological Puzzle of Mycorrhizal Associations Using Data from Annotated Collections and Environmental Samples - an Example of Saddle Fungi” Environmental microbiology reports 7, no. 4 (2015): 658–667.

Examples

library("ape")
##First plot a locus
as.matrix(rag1)->rr
read.tree(system.file("extdata","polypterus_trees.phy",package="PhyInformR"))->trees
trees[[1]]->tree
PlotTreeSI(tree,rr,3)
##Now plot another locus to compare
as.matrix(prumetalrates[1:1594])->candidate_locus
Plot.Another.TreeSI(tree,candidate_locus,3, color="red",type=3)

carolinafishes/PhyInformR documentation built on May 13, 2019, 12:50 p.m.