plotTreeDataMDS: Plot an MDS Plot of a Group of Trees

In HMPTrees: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

Description

This function can take any number of data sets and plots them on an MDS plot to show relative closeness to one another.

Usage

	plotTreeDataMDS(dataList, main = "Tree MDS Comparisons", calcMLE = TRUE, 
		mleTitles = NULL, dotColors = NULL, dotSizes = NULL, showNames = FALSE, 
		returnCoords = FALSE, data = NULL)

Arguments

dataList	A list of a data frames in which each column contains the rdp read counts for every taxa given in the row names.
main	A title for the MDS plot.
calcMLE	If 'FALSE' the MLEs for the data sets will not be calculated and plotted.
mleTitles	Deprecated. Replaced with the names in 'dataList'.
dotColors	The colors to be used when plotting the points and MLE points on the MDS plot.
dotSizes	A vector in which the first value is the data points CEX and the second value is the MLEs CEX.
showNames	When 'TRUE' the column name will be plotted above each corresponding point.
returnCoords	When 'TRUE' this function will return the x and y coordinates for every plotted point.
data	Deprecated. Replaced with dataList.

Value

A MDS plot of the data.

Author(s)

Berkley Shands, Patricio S. La Rosa, Elena Deych, William D. Shannon

Examples

	data(saliva)
	data(stool)
	
	plotTreeDataMDS(list(Saliva=saliva, Stool=stool))

Example output

HMPTrees documentation built on May 2, 2019, 4:02 p.m.