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microSTASIS (version 0.1.0)

Microbiota STability ASsessment via Iterative cluStering

Description

The toolkit 'STASIS' has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

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Version

Install

install.packages('microSTASIS')

Monthly Downloads

35

Version

0.1.0

License

GPL (>= 3)

Maintainer

Pedro S<c3><a1>nchez-S<c3><a1>nchez

Last Published

September 14th, 2021

Functions in microSTASIS (0.1.0)

pre_radarPC

Compute the PCA to the paired_times() output previously to visualize radar charts of principal components.
metadata_groups

Easily extract groups of individuals from metadata variables.
CV_iterative_clustering

Cross validation of the iterative Hartigan-Wong k-means clustering.
st_previz

Process the stabilitas() output to a new format ready for the visualization functions.
st_scatter

Plot a scatter and side boxplot of the stability results
CV_results

Compute the error or plot the stability values after CV_iterative_clustering().
st_evolution

Generate boxplots of the stability evolution throughout sampling times by groups
radarPC

Plot a radar chart of paired samples from one individual or from different groups.
paired_times

Generate a subset matrix with paired times.
st_heatmap

Plot a heatmap of the stability results
clr

Detected ASV from multiple individuals at four different sampling times.
iterative_clustering

Iterative Hartigan-Wong k-means clustering.
stabilitas

Extract the stability results of individuals from the output of iterative_clustering().