topAbsAbundPlot: Plot Top Taxa Abundance Normalized to Bacterial Load.
In patPRO: Visualizing Temporal Microbiome Data

Description Usage Arguments Details Author(s) References Examples

Uses the results from the top.abs.abund.data.frame function for graphing relative abundance of the top taxonomy normalized under the absolute bacterial load calculated from qPCR results.

topAbsAbundPlot(rel.abund.df, 
	patient.id, 
	subject.id.col="SubjectID", 
	tmpt.id.col="Time_point", 
	abs.abund.id.col="absolute_abund", 
	bac.id.col="Bacteria", 
	bac.load.col="bac_load", 
	y.lab="Relative Abundance of Bacterial Load", 
	x.lab="Time Point", 
	plot.title, 
	mark.events=FALSE, 
	mark.times, 
	mark.text="", 
	color.brewer.set="", 
	color.manual.set="", 
	legend.text.size = 7)

`rel.abund.df`	The `data.frame` from the top.abs.abund.data.frame function which will be used for plotting the top taxa.
`patient.id`	The patient identifier to specify the case which should be visualized.
`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".
`abs.abund.id.col`	Name of the column containing the normalized relative abundance information. Default is "absolute_abund".
`bac.id.col`	Name of the column containing the taxonomic identifiers for the dataset. Default is "Bacteria".
`bac.load.col`	Name of the column containing the bacterial load information. Default is "bac_load".
`y.lab`	Name of the y axis label to be used in the plot. Default is "Relative Abundance of Absolute Abundance".
`x.lab`	Name of the x axis label to be used in the plot. Default is "Time Point".
`plot.title`	The desired plot title.
`mark.events`	Specify whether arrows will be used to specify specific time events. Set as TRUE for using arrows. Default is FALSE.
`mark.times`	The time points to be marked with arrows when mark.events=TRUE. These numbers need to be set as a vector.
`mark.text`	The text to be used to annotate the arrow markers when mark.events=TRUE.
`color.brewer.set`	Name of the color brewer palet to use for plot coloring. Default value uses default colors.
`color.manual.set`	Name of the manually specified color palet to use for plot coloring. Default value uses default colors.
`legend.text.size`	Allows the user to manually set the figure legend text size digit. Default is size 7.

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")
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")
normTopTaxa <- topAbsAbundPlot(absAbundOutDf, 
	1, 
	bac.load.col="Num_Bacteria", 
	plot.title="Subject One Normalized Taxonomy", 
	color.brewer.set="Set2", 
	mark.events=TRUE, 
	mark.times=c(2,6), 
	mark.text="Surgery", 
	legend.text.size = 8)