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patPRO (version 1.1.0)

Visualizing Temporal Microbiome Data

Description

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

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Version

Install

install.packages('patPRO')

Monthly Downloads

5

Version

1.1.0

License

GPL-3

Maintainer

Geoffrey D Hannigan

Last Published

February 2nd, 2016

Functions in patPRO (1.1.0)

PatProMap

Test Mapping File Data Used as an Example for patPRO.
transposeRelAbund

Transpose a Data Frame.
mergeMapMetaData

Merge Mapping and Data Files
patproPlotTwo

Generate Patient Profile of Two Plots.
patPRO-package

Longitudinal Profiler of Microbiome Data
PatProBacLoad

Test Bacterial Load Data Used as an Example for patPRO.
patientMean

Calculate Mean Patient Values.
plotBacterialLoad

Plot Supplemental Bacterial Load Information.
plotNormalizedAlphaDiv

Plot Normalized Alpha Diversity.
patproPlotThree

Generate Patient Profile of Three Plots.
topRelAbundDataFrame

Format Top Taxa Data Frame for Graphing.
plotTopTaxa

Plot a Specific Patient Relative Abundance of Top Taxa.
topAbsAbundDataFrame

Format and Normalize Top Taxa and Bac Load for Plotting.
plotTopTaxaMean

Plot the Mean Relative Abundance of Top Taxa.
normalizeAlphaDiv

Normalize Alpha Diversity Values for Plotting.
PatProAlphaDiv

Test Alpha Diversity Data Used as an Example for patPRO.
topAbsAbundPlot

Plot Top Taxa Abundance Normalized to Bacterial Load.
PatProOTU

Test Relative Abundance Data Used as an Example for patPRO.