Function reference • LegATo

Plot and Visualize Longitudinal Microbial Data

plot_alluvial(): Plot an alluvial diagram of microbial relative abundance

plot_spaghetti(): Plot a spaghetti volatility plot of microbial abundance for a given taxon

plot_stacked_area(): Plot a stacked area chart of microbial relative abundance

plot_stacked_bar(): Plot a stacked bar chart of microbial relative abundance

plot_heatmap(): Plot a ComplexHeatmap.

distinctColors(): Generate a distinct palette for coloring different clusters.

Analyze Longitudinal Microbial Data

Conduct Hotelling’s T-squared tests, NMIT, and model data.

run_gee_model(): Compute Generalized Estimating Equations (GEEs) on longitudinal microbiome data

run_lmm_model(): Compute linear mixed-effects models (LMM) on longitudinal microbiome data

test_hotelling_t2(): Conduct a multivariate Hotelling's T-squared test

NMIT(): Nonparametric Microbial Interdependence Test (NMIT)

tscor(): Calculate within-subject OTU correlations

Manipulate Raw MAE Objects

Create, clean, and filter a MultiAssayExperiment object.

create_formatted_MAE(): Create a formatted MultiAssayExperiment compatible with LegATo

clean_animalcules_MAE(): Clean up taxon names in a MultiAssayExperiment

filter_animalcules_MAE(): Filter a MultiAssayExperiment to a top percentage of taxa and label the rest as "Other"

Reformat a MAE Object into a Data Frame

Take a animalcules-formatted MAE and reformat for visualizationa and analysis.

parse_MAE_SE(): Parse a MultiExperimentAssay object and extract the elements as data.frames

get_long_data(): Create a long data.frame from a MultiAssayExperiment counts object

get_stacked_data(): Create a long data.frame with grouped abundances from a MultiAssayExperiment counts object

get_summary_table(): Create a table summarizing reads aggregated by grouping variables on a unit

get_top_taxa(): Obtain a data.frame of ordered taxa abundances at a given level