Package index
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add_alpha() - Add alpha transparency to hex colors
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build_dendrogram() - Build a dendrogram (and leaf order) from an ASV matrix
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classify_taxa_patterns() - Classify taxa by abundance patterns across groups
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combine_dendrogram_alluvial() - Combine dendrogram and alluvial plot with alignment and flexible legend placement
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create_alluvial_dendrogram_plot() - Create an aligned alluvial + dendrogram figure (full workflow wrapper)
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create_alluvial_plot() - Create an alluvial plot via the full workflow wrapper
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create_grouped_matrix() - Create grouped ASV matrix by averaging within groups
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em_metadata - Example sample metadata
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em_otu - Example OTU matrix
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example_microbiome - Example microbiome dataset
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extract_legend_grob() - Extract a legend grob from a ggplot
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generate_alluvial_palette() - Generate a color palette for alluvial plots from tax_color keys
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generate_grouped_palette() - Generate grouped palettes using HCL colors
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generate_palette_hcl() - Generate HCL color palette for taxonomic visualization
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plot_alluvial() - Create an alluvial (Sankey) plot of taxonomic composition across groups
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plot_dendrogram() - Plot a dendrogram as ggplot with optional tip aesthetics (color/fill/shape/size) and labels
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plot_taxonomic_barplot() - Create stacked taxonomic barplots with optional faceting and strip theming
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prepare_alluvial_data() - Aggregate microbiome data for alluvial plot visualization
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process_barplot_data() - Process barplot data at specified taxonomic level
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replace_incertae_sedis_NAs() - Normalize Incertae sedis and fill missing taxonomy ranks
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theme_phylopal() - A clean minimal theme for phyloPal plots