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ggpicrust2 (version 2.5.2)

Make 'PICRUSt2' Output Analysis and Visualization Easier

Description

Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) .

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Install

install.packages('ggpicrust2')

Monthly Downloads

723

Version

2.5.2

License

MIT + file LICENSE

Issues

91

Pull Requests

1

Stars

156

Forks

26

Maintainer

Chen Yang

Last Published

August 25th, 2025

Functions in ggpicrust2 (2.5.2)

ggpicrust2

This function integrates pathway name/description annotations, ten of the most advanced differential abundance (DA) methods, and visualization of DA results.
ko_abundance

KO Abundance Dataset
create_heatmap_plot

Create heatmap visualization of GSEA results
get_significance_stars

Get Significance Stars
create_legend_theme

Create Enhanced Legend Theme
ggpicrust2_extended

Integrated analysis with ggpicrust2 including GSEA
import_MicrobiomeAnalyst_daa_results

Import Differential Abundance Analysis (DAA) results from MicrobiomeAnalyst
gsea_pathway_annotation

Annotate GSEA results with pathway information
pathway_gsea

Gene Set Enrichment Analysis for PICRUSt2 output
pathway_heatmap

Create pathway heatmap with support for multiple grouping variables
metacyc_abundance

MetaCyc Abundance Dataset
ko2kegg_abundance

Convert KO abundance in picrust2 export files to KEGG pathway abundance
pathway_pca

Perform Principal Component Analysis (PCA) on functional pathway abundance data
prepare_gene_sets

Prepare gene sets for GSEA
metadata

Metadata for ggpicrust2 Demonstration
kegg_abundance

KEGG Abundance Dataset
resolve_annotation_overlaps

Detect and Resolve Annotation Overlaps
preview_color_theme

Preview Color Theme
smart_color_selection

Smart Color Selection
pathway_errorbar_table

Generate Abundance Statistics Table for Pathway Analysis
legend_annotation_utils

Legend and Annotation Utilities for ggpicrust2
run_fgsea

Run fast GSEA implementation
safe_extract

Safely Extract Elements from a List
pathway_errorbar

The function pathway_errorbar() is used to visualize the results of functional pathway differential abundance analysis as error bar plots.
validate_abundance_data

Validate abundance data for PICRUSt compatibility
pathway_daa

Differential Abundance Analysis for Predicted Functional Pathways
pathway_annotation

Pathway information annotation
visualize_gsea

Visualize GSEA results
validate_group_sizes

Validate group sizes for statistical analysis
compare_daa_results

Compare the Consistency of Statistically Significant Features
calculate_smart_text_size

Smart Text Size Calculator
create_basic_go_mapping

Create basic GO mapping for microbiome analysis
compare_metagenome_results

Compare Metagenome Results
compare_gsea_daa

Compare GSEA and DAA results
color_themes

Color Theme System for ggpicrust2
create_gradient_colors

Create Gradient Colors
format_pvalue_smart

Smart P-value Formatting
daa_results_df

DAA Results Dataset
create_dendrogram

Create dendrogram plot from hierarchical clustering
generate_nested_colors

Generate colors for nested grouping variables
calculate_rank_metric

Calculate rank metric for GSEA
create_empty_plot

Create empty plot for edge cases
get_available_themes

Get Available Color Themes
get_color_theme

Get Color Theme
daa_annotated_results_df

Differentially Abundant Analysis Results with Annotation
create_network_plot

Create network visualization of GSEA results
create_pathway_class_theme

Create Pathway Class Annotation Theme
get_significance_colors

Get Significance Colors