R: Plot Top Taxa Abundance Normalized to Bacterial Load.

topAbsAbundPlot {patPRO} | R Documentation

## 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.

### 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")
    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)

[Package patPRO version 1.1.0 Index]