patPRO: Visualizing Temporal Microbiome Data

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Quickly and easily visualize longitudinal microbiome profiles using standard output from the QIIME microbiome analysis toolkit (see <http://qiime.org> for more information).

Author
Hannigan GD, Loesche MA, Hodkinson BP, Mehta S, Grice EA
Date of publication
2016-02-02 17:25:52
Maintainer
Geoffrey D Hannigan <ghanni@upenn.edu>
License
GPL-3
Version
1.1.0

View on CRAN

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.

Files in this package

patPRO
patPRO/inst
patPRO/inst/extdata
patPRO/inst/extdata/ExampleQiimeOtuTrauma.tsv
patPRO/inst/extdata/ExampleQiimeAlphaTrauma.tsv
patPRO/inst/extdata/ExampleQiimeMapTrauma.csv
patPRO/inst/extdata/ExampleQiimeBacLoadTrauma.tsv
patPRO/NAMESPACE
patPRO/data
patPRO/data/PatProOTU.RData
patPRO/data/PatProBacLoad.RData
patPRO/data/PatProAlphaDiv.RData
patPRO/data/PatProMap.RData
patPRO/R
patPRO/R/PatPro1.R
patPRO/MD5
patPRO/DESCRIPTION
patPRO/man
patPRO/man/patproPlotTwo.Rd
patPRO/man/plotNormalizedAlphaDiv.Rd
patPRO/man/topAbsAbundPlot.Rd
patPRO/man/plotTopTaxaMean.Rd
patPRO/man/normalizeAlphaDiv.Rd
patPRO/man/mergeMapMetaData.Rd
patPRO/man/plotTopTaxa.Rd
patPRO/man/PatProBacLoad.Rd
patPRO/man/topAbsAbundDataFrame.Rd
patPRO/man/patproPlotThree.Rd
patPRO/man/transposeRelAbund.Rd
patPRO/man/patientMean.Rd
patPRO/man/PatProMap.Rd
patPRO/man/PatProAlphaDiv.Rd
patPRO/man/PatPro-package.Rd
patPRO/man/plotBacterialLoad.Rd
patPRO/man/topRelAbundDataFrame.Rd
patPRO/man/PatProOTU.Rd