patPRO: Visualizing Temporal Microbiome Data
Version 1.1.0

Quickly and easily visualize longitudinal microbiome profiles using standard output from the QIIME microbiome analysis toolkit (see for more information).

AuthorHannigan GD, Loesche MA, Hodkinson BP, Mehta S, Grice EA
Date of publication2016-02-02 17:25:52
MaintainerGeoffrey D Hannigan <ghanni@upenn.edu>
LicenseGPL-3
Version1.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("patPRO")

Popular man pages

mergeMapMetaData: Merge Mapping and Data Files
PatProOTU: Test Relative Abundance Data Used as an Example for patPRO.
plotNormalizedAlphaDiv: Plot Normalized Alpha Diversity.
plotTopTaxa: Plot a Specific Patient Relative Abundance of Top Taxa.
plotTopTaxaMean: Plot the Mean Relative Abundance of Top Taxa.
topAbsAbundDataFrame: Format and Normalize Top Taxa and Bac Load for Plotting.
transposeRelAbund: Transpose a Data Frame.
See all...

All man pages Function index File listing

Man pages

mergeMapMetaData: Merge Mapping and Data Files
normalizeAlphaDiv: Normalize Alpha Diversity Values for Plotting.
patientMean: Calculate Mean Patient Values.
PatProAlphaDiv: Test Alpha Diversity Data Used as an Example for patPRO.
PatProBacLoad: Test Bacterial Load Data Used as an Example for patPRO.
PatProMap: Test Mapping File Data Used as an Example for patPRO.
PatProOTU: Test Relative Abundance Data Used as an Example for patPRO.
PatPro-package: Longitudinal Profiler of Microbiome Data
patproPlotThree: Generate Patient Profile of Three Plots.
patproPlotTwo: Generate Patient Profile of Two Plots.
plotBacterialLoad: Plot Supplemental Bacterial Load Information.
plotNormalizedAlphaDiv: Plot Normalized Alpha Diversity.
plotTopTaxa: Plot a Specific Patient Relative Abundance of Top Taxa.
plotTopTaxaMean: Plot the Mean Relative Abundance of Top Taxa.
topAbsAbundDataFrame: Format and Normalize Top Taxa and Bac Load for Plotting.
topAbsAbundPlot: Plot Top Taxa Abundance Normalized to Bacterial Load.
topRelAbundDataFrame: Format Top Taxa Data Frame for Graphing.
transposeRelAbund: Transpose a Data Frame.

Functions

Files

inst
inst/extdata
inst/extdata/ExampleQiimeOtuTrauma.tsv
inst/extdata/ExampleQiimeAlphaTrauma.tsv
inst/extdata/ExampleQiimeMapTrauma.csv
inst/extdata/ExampleQiimeBacLoadTrauma.tsv
NAMESPACE
data
data/PatProOTU.RData
data/PatProBacLoad.RData
data/PatProAlphaDiv.RData
data/PatProMap.RData
R
R/PatPro1.R
MD5
DESCRIPTION
man
man/patproPlotTwo.Rd
man/plotNormalizedAlphaDiv.Rd
man/topAbsAbundPlot.Rd
man/plotTopTaxaMean.Rd
man/normalizeAlphaDiv.Rd
man/mergeMapMetaData.Rd
man/plotTopTaxa.Rd
man/PatProBacLoad.Rd
man/topAbsAbundDataFrame.Rd
man/patproPlotThree.Rd
man/transposeRelAbund.Rd
man/patientMean.Rd
man/PatProMap.Rd
man/PatProAlphaDiv.Rd
man/PatPro-package.Rd
man/plotBacterialLoad.Rd
man/topRelAbundDataFrame.Rd
man/PatProOTU.Rd
patPRO documentation built on May 19, 2017, 11:49 a.m.

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