Package: ggpicrust2 2.5.17

ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

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) <doi:10.1093/bioinformatics/btad470>.

Authors:Chen Yang [aut, cre], Liangliang Zhang [aut]

ggpicrust2_2.5.17.tar.gz
ggpicrust2_2.5.17.zip(r-4.7)ggpicrust2_2.5.17.zip(r-4.6)ggpicrust2_2.5.17.zip(r-4.5)
ggpicrust2_2.5.17.tgz(r-4.6-any)ggpicrust2_2.5.17.tgz(r-4.5-any)
ggpicrust2_2.5.17.tar.gz(r-4.7-any)ggpicrust2_2.5.17.tar.gz(r-4.6-any)
ggpicrust2_2.5.17.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggpicrust2/json (API)

# Install 'ggpicrust2' in R:

install.packages('ggpicrust2', repos = c('https://cafferychen777.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cafferychen777/ggpicrust2/issues

Datasets:

daa_annotated_results_df - Differentially Abundant Analysis Results with Annotation
daa_results_df - DAA Results Dataset
ec_reference - EC Number Reference Dataset
kegg_abundance - KEGG Abundance Dataset
kegg_pathway_reference - KEGG Pathway Name Reference Dataset
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
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

On CRAN:

microbiome metagenomics software 16s-rrna bioinformatics data-visualization differential-abundance functional-data functional-prediction ggplot2 gut-microbiome kegg metagenomic-analysis microbiota pathway-analysis phyloseq picrust2 tax4fun2 visualization

9.73 score 198 stars 239 scripts 1.4k downloads 37 exports 71 dependencies

Last updated from:a38a0a2880. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	302
source / vignettes	OK	333
linux-release-x86_64	OK	275
macos-release-arm64	OK	146
macos-oldrel-arm64	OK	177
windows-devel	OK	173
windows-release	OK	193
windows-oldrel	OK	177
wasm-release	OK	262

Exports:aggregate_taxa_contributions calculate_smart_text_size compare_daa_results compare_gsea_daa compare_metagenome_results create_gradient_colors create_legend_theme create_pathway_class_theme format_pvalue_smart get_available_themes get_color_theme get_significance_colors get_significance_stars ggpicrust2 gsea_pathway_annotation import_MicrobiomeAnalyst_daa_results ko2kegg_abundance pathway_annotation pathway_daa pathway_errorbar pathway_errorbar_table pathway_gsea pathway_heatmap pathway_pca pathway_ridgeplot pathway_volcano prepare_gene_sets preview_color_theme read_contrib_file read_pathway_contrib_file read_strat_file resolve_annotation_overlaps safe_extract smart_color_selection taxa_contribution_bar taxa_contribution_heatmap visualize_gsea

Dependencies:aplot base64enc bit bit64 cachem cli clipr cpp11 crayon digest dplyr farver fastmap fs generics ggforce ggfun ggh4x ggplot2 ggplotify ggprism ggraph ggrepel glue graphlayouts gridExtra gridGraphics gtable hms igraph isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix memoise patchwork pillar pkgconfig polyclip prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr rlang S7 scales stringi stringr systemfonts tibble tidygraph tidyr tidyselect tweenr tzdb utf8 vctrs viridis viridisLite vroom withr yulab.utils

Using ggpicrust2

Rendered fromusing_ggpicrust2.Rmdusingknitr::rmarkdown

Last update: 2026-05-05
Started: 2023-05-30

Gene Set Enrichment Analysis with ggpicrust2

Rendered fromgsea_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-01-04
Started: 2025-07-23

Citation

Development and contributors

Readme and manuals

Help Manual

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