Package index
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ggpicrust2() - This function integrates pathway name/description annotations, ten of the most advanced differential abundance (DA) methods, and visualization of DA results.
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ko2kegg_abundance() - Convert KO abundance in picrust2 export files to KEGG pathway abundance
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pathway_daa() - Differential Abundance Analysis for Predicted Functional Pathways
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pathway_annotation() - Pathway information annotation
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pathway_errorbar() - The function pathway_errorbar() is used to visualize the results of functional pathway differential abundance analysis as error bar plots.
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pathway_errorbar_table() - Generate Abundance Statistics Table for Pathway Analysis
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pathway_heatmap() - Create pathway heatmap with support for multiple grouping variables
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pathway_pca() - Perform Principal Component Analysis (PCA) on functional pathway abundance data
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pathway_volcano() - Volcano Plot for Pathway Differential Abundance Analysis
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pathway_ridgeplot() - Ridge Plot for GSEA Results
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compare_daa_results() - Compare the Consistency of Statistically Significant Features
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compare_metagenome_results() - Compare Metagenome Results
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read_contrib_file() - Read PICRUSt2 contribution file
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read_pathway_contrib_file() - Read PICRUSt2 pathway-level contribution file
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read_strat_file() - Read PICRUSt2 stratified abundance file
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aggregate_taxa_contributions() - Aggregate taxa contributions for visualization
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taxa_contribution_bar() - Stacked bar plot of taxa contributions
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taxa_contribution_heatmap() - Heatmap of taxa contributions across functions
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pathway_gsea() - Gene Set Enrichment Analysis for PICRUSt2 output
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visualize_gsea() - Visualize GSEA results
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compare_gsea_daa() - Compare GSEA and DAA results
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gsea_pathway_annotation() - Annotate GSEA results with pathway information
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prepare_gene_sets() - Prepare gene sets for GSEA
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metadata - Metadata for ggpicrust2 Demonstration
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ko_abundance - KO Abundance Dataset
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kegg_abundance - KEGG Abundance Dataset
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metacyc_abundance - MetaCyc Abundance Dataset
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daa_results_df - DAA Results Dataset
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daa_annotated_results_df - Differentially Abundant Analysis Results with Annotation
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ko_reference - KEGG Orthology (KO) Reference Dataset
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kegg_pathway_reference - KEGG Pathway Name Reference Dataset
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ec_reference - EC Number Reference Dataset
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metacyc_reference - MetaCyc Pathway Reference Dataset
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ko_to_kegg_reference - KO to KEGG Pathway Reference Data
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ko_to_go_reference - KO to GO Reference Mapping Dataset
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metacyc_to_ec_reference - MetaCyc Pathway to EC Number Mapping Dataset
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import_MicrobiomeAnalyst_daa_results() - Import Differential Abundance Analysis (DAA) results from MicrobiomeAnalyst
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color_themes - Color Theme System for ggpicrust2
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legend_annotation_utils - Legend and Annotation Utilities for ggpicrust2
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create_gradient_colors() - Create Gradient Colors
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create_legend_theme() - Create Enhanced Legend Theme
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create_pathway_class_theme() - Create Pathway Class Annotation Theme
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get_available_themes() - Get Available Color Themes
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get_color_theme() - Get Color Theme
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get_significance_colors() - Get Significance Colors
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get_significance_stars() - Get Significance Stars
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calculate_smart_text_size() - Smart Text Size Calculator
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preview_color_theme() - Preview Color Theme
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format_pvalue_smart() - Smart P-value Formatting
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smart_color_selection() - Smart Color Selection
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resolve_annotation_overlaps() - Detect and Resolve Annotation Overlaps
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safe_extract() - Safely Extract Elements from a List