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ggpicrust2 vignettes

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install.packages('ggpicrust2')

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Version

2.3.2

License

MIT + file LICENSE

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Maintainer

Chen Yang

Last Published

July 16th, 2025

Functions in ggpicrust2 (2.3.2)

ggpicrust2

This function integrates pathway name/description annotations, ten of the most advanced differential abundance (DA) methods, and visualization of DA results.
ggpicrust2_extended

Integrated analysis with ggpicrust2 including GSEA
pathway_heatmap

Create pathway heatmap
import_MicrobiomeAnalyst_daa_results

Import Differential Abundance Analysis (DAA) results from MicrobiomeAnalyst
gsea_pathway_annotation

Annotate GSEA results with pathway information
compare_daa_results

Compare the Consistency of Statistically Significant Features
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.
safe_extract

Safely Extract Elements from a List
run_fgsea

Run fast GSEA implementation
pathway_pca

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

Prepare gene sets for GSEA
ko2kegg_abundance

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

KEGG Abundance Dataset
visualize_gsea

Visualize GSEA results
compare_gsea_daa

Compare GSEA and DAA results
create_heatmap_plot

Create heatmap visualization of GSEA results
compare_metagenome_results

Compare Metagenome Results
pathway_annotation

Pathway information annotation
create_network_plot

Create network visualization of GSEA results
daa_annotated_results_df

Differentially Abundant Analysis Results with Annotation
daa_results_df

DAA Results Dataset
ko_abundance

KO Abundance Dataset
calculate_rank_metric

Calculate rank metric for GSEA
pathway_gsea

Gene Set Enrichment Analysis for PICRUSt2 output
metacyc_abundance

MetaCyc Abundance Dataset
metadata

Metadata for ggpicrust2 Demonstration