topRelAbundDataFrame: Format Top Taxa Data Frame for Graphing.
In patPRO: Visualizing Temporal Microbiome Data

Description Usage Arguments Details Author(s) References Examples

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

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

`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".

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.

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

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

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)