patPRO (version 1.1.0)

topAbsAbundPlot: Plot Top Taxa Abundance Normalized to Bacterial Load.

Description

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.

Usage

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)

Arguments

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.

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.

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")
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)