R: Normalize Alpha Diversity Values for Plotting.

normalizeAlphaDiv {patPRO} | R Documentation

## Normalize Alpha Diversity Values for Plotting.

### Description

This function normalizes the alpha diversity values of a single patient's time course to the initial time point. The initial time point is used as 100 percent. This allows for plotting of multiple alpha diversity metrics on a single plot, despite differences in value magnitude.

### Usage

    normalizeAlphaDiv(alpha.div.input,
    	alpha.div.metric,
    	subject.id.range,
    	subject.id.col="SubjectID",
    	tmpt.id.col="Time_point")

### Arguments

`alpha.div.input` | The `data.frame` from Qiime containing the alpha diversity information for the dataset. This should also include subject ID and time point information.
`alpha.div.metric` | The name(s) of the columns containing the alpha diversity metric information to be used for normalization.
`subject.id.range` |
`subject.id.col` | Name of the subject ID column found in alpha.div.input. Default is "SubjectID".
`tmpt.id.col` | Name of the time point column found in alpha.div.input. Default is "Time_point".

### Details

Package: | patPRO
Type: | Package
Version: | 1.0.0
Date: | 2015-09-18
License: | GPLv3

An overview of how to use the package, including the most important functions, is included in the supplemental R notebook patPROExampleWorkflow.html.

### Author(s)

Geoffrey Hannigan <ghanni@upenn.edu>, Loesche MA, Hodkinson BP, Mehta S, Elizabeth Grice <egrice@upenn.edu>

### References

patPRO: An R package for the visualization of longitudinal microbiome data. Hannigan GD, Loesche MA, Hodkinson BP, Mehta S, Grice EA.

### Examples

    data("PatProAlphaDiv",package="patPRO")
    data("PatProMap",package="patPRO")
    mergedMapAlpha <- mergeMapMetaData(map.file=PatProMap,
    	merging.file=PatProAlphaDiv,
    	map.sub.id="SubjectID",
    	map.tmpt="Time_point",
    	map.smpl.id="SampleID",
    	sample.id.col="SampleID")
    testNormAlphaDiv <- normalizeAlphaDiv(mergedMapAlpha, c("chao1","shannon"), 1)

[Package patPRO version 1.1.0 Index]