topAbsAbundDataFrame {patPRO}R Documentation

Format and Normalize Top Taxa and Bac Load for Plotting.

Description

Calcualte the top taxa relative abundance normalized to the overall bacterial load. Prepare the data frame for graphing.

Usage

topAbsAbundDataFrame(rel.abund, 
	bac.load, 
	bac.load.id="bac_load", 
	abund.id.col="Abundance", 
	subject.id.col="SubjectID", 
	tmpt.id.col="Time_point", 
	bacteria.id.col="Bacteria")

Arguments

rel.abund

The transposed relative abundance data.frame to be used for graphing of microbial relative abundances.

bac.load

The data.frame containing the bacterial load information, as well as the subject IDs and time points associated with those load data points.

bac.load.id

Name of the bacterial load value column. Default is "bac_load".

abund.id.col

Name of the column containing the relative abundance values for the top taxa relative abundance. Default is "Abundance".

subject.id.col

Name of the subject ID column. Default is "SubjectID".

tmpt.id.col

Name of the time point column. Default is "Time_point".

bacteria.id.col

Name of the column to contain the bacterial load values. Default is "Bacteria".

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")
data("PatProBacLoad",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")
top5RelAbund <- topRelAbundDataFrame(x=mergedMapTransRA, top.taxa.num=5)
mergedMapBacLoad <- mergeMapMetaData(map.file=PatProMap, 
	merging.file=PatProBacLoad, 
	map.sub.id="SubjectID", 
	map.tmpt="Time_point", 
	map.smpl.id="SampleID", 
	sample.id.col="SampleID")
absAbundOutDf <- topAbsAbundDataFrame(top5RelAbund, mergedMapBacLoad, bac.load.id="Num_Bacteria")
[Package patPRO version 1.1.0 Index]