R: Plot the Mean Relative Abundance of Top Taxa.

plotTopTaxaMean {patPRO} | R Documentation

## Plot the Mean Relative Abundance of Top Taxa.

### 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 <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")
    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)

[Package patPRO version 1.1.0 Index]