R: Format Top Taxa Data Frame for Graphing.

topRelAbundDataFrame {patPRO} | R Documentation

## Format Top Taxa Data Frame for Graphing.

### Description

Prepare the data frame for graphing of the relative abundances of the defined top taxa using the transposed output (originally from Qiime) using 'transposeRelAbund'.

### Usage

    topRelAbundDataFrame(x,
    	top.taxa.num,
    	subject.id.col="SubjectID",
    	sample.id.col="SampleID",
    	tmpt.id.col="Time_point")

### Arguments

`x` | The transposed relative abundance `data.frame` to be used for graphing of microbial relative abundances.
`top.taxa.num` | The number of top taxa requested.
`subject.id.col` | Name of the subject ID column found in x. Default is "SubjectID".
`sample.id.col` | Name of the sample ID column found in x. Default is "SampleID".
`tmpt.id.col` | Name of the time point column found in x. 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("PatProOTU",package="patPRO")
    data("PatProMap",package="patPRO")
    transTestRelAbund <- transposeRelAbund(PatProOTU)
    mergedMapTransRA <- mergeMapMetaData(map.file=PatProMap,
    	merging.file=transTestRelAbund,
    	map.sub.id="SubjectID",
    	map.tmpt="Time_point",
    	map.smpl.id="SampleID",
    	sample.id.col="SampleID")
    top5_rel_abund <- topRelAbundDataFrame(x=mergedMapTransRA, top.taxa.num=5)

[Package patPRO version 1.1.0 Index]