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Last data update: 2014.03.03

R: Create and Plot a Tree from a Data Set

createAndPlot

R Documentation

Create and Plot a Tree from a Data Set

Description

This function combines the createTrees and plotTree functions to create and plot a set of trees.

Usage

	createAndPlot(data, samples = 1, level = "genus", colors, divisions, main, 
		sub, showTipLabel = TRUE, showNodeLabel = FALSE, displayLegend = TRUE, 
		onePerPage = FALSE)

Arguments

`data`	A data frame in which each column contains the rdp read counts for every taxa given in the row names.
`samples`	A numeric vector that is used to select a single (or several) tree(s) out of a data set. A value of 0 will select all trees.
`level`	The depth the tree creation will go down to (kingdom, phylum, class, order, family, genus, species, subspecies). 'genus' is the default.
`colors`	A vector of colors to be applied to the branches in the plot.
`divisions`	A vector of numbers to be used as break points to assign different colors.
`main`	A custom title(s) for the plot(s). The default value is the column names.
`sub`	A custom subtitle for the plot.
`showTipLabel`	Hides the tip labels if 'FALSE' otherwise it shows all non-zero tip labels.
`showNodeLabel`	Hides the interior node labels if 'FALSE' otherwise it shows all non-zero node labels.
`displayLegend`	Enables the display of a legend of the branch colors and divisions when 'TRUE'.
`onePerPage`	If 'TRUE' one tree will be plotted per page, if 'FALSE' four will be displayed per page.

Details

Notes:

For 'level' k, p, c, o, f, g, s and ss can be used in place of kingdom, phylum, class, order, family, genus, species and subspecies respectively.
The values for division should directly relate to the values of your data, i.e. if your data ranges from 0 to 50000 reads you should adjust the divisions to fit your data.

Value

A plot of the tree(s).

Author(s)

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

Examples

	data(saliva)
	
	### Plots the trees in column 2 and 3 in 'Saliva'
	createAndPlot(saliva, c(2:3))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(HMPTrees)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HMPTrees/createAndPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: createAndPlot
> ### Title: Create and Plot a Tree from a Data Set
> ### Aliases: createAndPlot
> 
> ### ** Examples
> 
> 	data(saliva)
> 	
> 	### Plots the trees in column 2 and 3 in 'Saliva'
> 	createAndPlot(saliva, c(2:3))
NULL
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>