# Make 'PICRUSt2' Output Analysis and Visualization Easier

## Documentation for package ‘ggpicrust2’ version 2.5.17

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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