The package paaPack provides R implementation of the Principal Amalgamation Analysis for microbiome data

Overview

The paaPack is designed to perform hierarchical Principal Amalgamation Analysis (HPAA) with or without the guidance of taxonomic tree structure, and provide several useful graphical tools for visualizing the results of HPAA, including

1. hierarchical dendrograms to visualize the full path of amalgamations,
2. the scree plot showing the percentage change in the diversity loss along with the changes of number of compositions, and
3. the ordination plot showing the changes in the between-sample distance patterns before and after HPAA with any given number of principal compositions (PC).

Installation

One may install the latest version under development as follows (Rtools may be required for installation):

install.packages(c("devtools"))
devtools::install_github("LiYanStat/paaPack")

Get Started

The paaPack provides a main function hPAA() to perform the hierarchical Principal Amalgamation Analysis (HPAA). To use the function, the analyst should provide:

• The compositional data with row representing compositions for each subject and column recording the original components/taxa.

• The taxonomic tree structure as a vector with dimension same as the number of taxa. The format of the taxonomic vector is the same as output format of the commonly used bioinformatics data processing software Mothur. That is, each element of the vector denotes the full taxonomic ranks from kingdom to genus, species level of the taxon, with ranks separated by semicolon. For example a typical element of the taxonomic vector could be k_Bacteria;p_Actinobacteria;c_Actinobacteria;o_Bifidobacteriales;f_Bifidobacteriaceae;g_Bifidobacterium;s_longum. The taxonomic structure is optional. If taxonomy is not provided, the unconstrained HPAA without tree guidance is performed.

• The diversity measures used in the HPAA analysis, and indicate whether strong or weak taxonomic hierarchy is applied in the analysis.

Then a set of plotting methods are provided taking the object of class "hPAA" from the hPAA() as input, including plotHPAA() for the dendrogram showing the full path of hierarchical amalgamation, plotLine() for the scree plot showing the percentage change in the diversity loss with the changing in the number of principal compositions, and plotMDS() for the ordination plot showing the changes in the between-sample distance patterns before and after HPAA. In each function, a group of graphical arguments for shaping the figures could be specified. For details, the analyst could refer to the documentations of the functions using help().

library(paaPack)
#### functions in paaPack
help(hPAA)  #### fit HPAA models
help(plotHPAA)  #### dendrogram showing the hierarchical amalgamation
help(plotLine)  #### scree plot showing the percentage
help(plotMDS)  #### ordination plot

Demo

A detailed demo with numerical examples is provided as Rmarkdown file demo/paaPack.rmd for reference.