HMPTrees (version 1.4)

plotTreeDataMDS: Plot an MDS Plot of a Group of Trees

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.

Examples

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