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

Description Usage Arguments Value Author(s) References Examples

Description

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

Usage

1
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

1
2
3
4
5
6
7
8
9
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.