patproPlotThree: Generate Patient Profile of Three Plots.

In patPRO: Visualizing Temporal Microbiome Data

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 <[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

# 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")

Example output

No id variables; using all as measure variables
Using SampleID as id variables
Warning: Ignoring unknown aesthetics: width

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