R: Generate Patient Profile of Three Plots.

patproPlotThree {patPRO} | R Documentation

## Generate Patient Profile of Three Plots.

### Description

Use this function to generate a patient profile containing three figures. The figures included are the alpha diversity, bacterial load, and top taxa plots over time. This should be used when bacterial load information is available, and the normalized relative abundance plot is not desired.

### Usage

    patproPlotThree(alpha.div.plot,
    	bac.load.plot,
    	top.taxa.plot,
    	patpro.plot.title,
    	legend.one.h=0.77,
    	legend.two.h=0.25)

### Arguments

`alpha.div.plot` | The alpha diversity plot to be used in the patient profile.
`bac.load.plot` | The bacterial load plot to be used in the patient profile.
`patpro.plot.title` | The desired plot title.
`legend.one.h` | Allows the user to manually set the height of the first figure legend (decimal digit between 0 and 1). Very important if adjusting legend text size. Defalut is 0.77.
`legend.two.h` | Allows the user to manually set the height of the second figure legend (decimal digit between 0 and 1). Very important if adjusting legend text size. Defalut is 0.25.
`top.taxa.plot` | The relative abundance plot to be used in the patient profile.

### 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

    # Plot individual patient
    data("PatProAlphaDiv",package="patPRO")
    data("PatProMap",package="patPRO")
    data("PatProOTU",package="patPRO")
    data("PatProBacLoad",package="patPRO")
    # Alpha Diversity
    mergedMapAlpha <- mergeMapMetaData(map.file=PatProMap,
      merging.file=PatProAlphaDiv,
      map.sub.id="SubjectID",
      map.tmpt="Time_point",
      map.smpl.id="SampleID",
      sample.id.col="SampleID")
    testNormAlphaDiv <- normalizeAlphaDiv(mergedMapAlpha, c("chao1","shannon"), 1)
    alphaDivPlot <- plotNormalizedAlphaDiv(testNormAlphaDiv,
      c("chao1","shannon"),
      plot.title="Subject One Diversity",
      color.brewer.set="Set2",
      legend.text.size = 12)
    # Bacterial Load
    mergedMapBacLoad <- mergeMapMetaData(map.file=PatProMap,
      merging.file=PatProBacLoad,
      map.sub.id="SubjectID",
      map.tmpt="Time_point",
      map.smpl.id="SampleID",
      sample.id.col="SampleID")
    bacLoad <- plotBacterialLoad(mergedMapBacLoad,
      1,
      bac.load.col="Num_Bacteria",
      plot.title="Subject One Bacterial Load")
    # Taxa Relative Abundance
    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)
    topTaxa <- plotTopTaxa(top5RelAbund,
      1,
      plot.title="Subject One Taxonomy",
      color.brewer.set="Set2",
      mark.events=TRUE,
      mark.times=c(2,6),
      mark.text="Surgery",
      legend.text.size=8)
    # Plot three
    patproPlotThree(alphaDivPlot, bacLoad, topTaxa, "Subject One Profile")

[Package patPRO version 1.1.0 Index]