plotTopTaxaMean: Plot the Mean Relative Abundance of Top Taxa.

In patPRO: Visualizing Temporal Microbiome Data

Description

Uses the results from the top.rel.abund.data.frame and the patient.mean function for graphing relative abundance of the top taxonomy. This is used seperate from the plotTopTaxaMean function because it uses mean values.

Usage

plotTopTaxaMean(top.taxa.data.frame, 
	tmpt.id.col="Time_point", 
	y.lab="Percent Relative Abundance", 
	x.lab="Time Point", plot.title, 
	mark.events=FALSE, 
	mark.times, 
	mark.text="", 
	color.brewer.set="", 
	color.manual.set="", 
	legend.text.size = 7)

Arguments

top.taxa.data.frame	The data.frame from the top.rel.abund.data.frame function which will be used for plotting the top taxa.
tmpt.id.col	Name of the time point column found in x. Default is "Time_point".
y.lab	Name of the y axis label to be used in the plot. Default is "Percent Relative 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.

Author(s)

Geoffrey Hannigan <[e-mail]>, Loesche MA, Hodkinson BP, Mehta S, Elizabeth Grice <[e-mail]>

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")
top5RelAbund <- topRelAbundDataFrame(x=mergedMapTransRA, top.taxa.num=5)
topTaxaMean <- patientMean(x=top5RelAbund, sub.range=c(1:5), metric.col="Bacteria")
topTaxaMeanPlot <- plotTopTaxaMean(topTaxaMean, 
	plot.title="Mean Taxonomy For Subjects 1-5", 
	color.brewer.set="Set2", 
	legend.text.size = 8)

Example output

Using SampleID as id variables
Warning: Ignoring unknown aesthetics: width

patPRO documentation built on May 1, 2019, 10:56 p.m.