ggpicrust2

2.5.17

Make 'PICRUSt2' Output Analysis and Visualization Easier

0packages depend

11.8Kdownloads / year

59.0%test coverage

10/13checks pass

Overview

About

Maintained by Chen YangFirst published 2023-03-2419 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("ggpicrust2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("cafferychen777/ggpicrust2")

Development version from cafferychen777/ggpicrust2. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ggpicrust2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ggpicrust2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ggpicrust2

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1ERROR2NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-oldrel-macos-arm64

Slowest check: 6.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.45

59.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-03-10
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 2,976 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 35%
Documented parameters: 99%
Return-value docs: 100%
References docs: 12%

Downloads

11.8K

CRAN downloads in the past year

Rank #3,258 · ~32/day · ~980/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.9K90 days

11.8K1 year

Compare downloads with other packages →

Also on281 r2u34 autocran

Repository

GitHub ↗ cafferychen777/ggpicrust2

198Stars

26Forks

5Open issues

3Open PRs

18Releases

523Commits

5Contributors

picrust2functional-datametagenomic-analysisvisualizationtax4fun216s-rrnametagenomicsmicrobiome

523 commits · Last activity 2026-06-30 · 0% stars, 30d

Stars over time

2025-07-22 · 1422026-07-07 · 198

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/cafferychen777/ggpicrust2 on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

renvdata-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

43 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (19)

aplot dplyr ggplot2gridggh4x readr tibble tidyr ggprism patchwork ggplotify magrittr progressstatsmethodsgrDevicestidygraph ggraphutils

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 15,636 (78%)Rd 3,887 (19%)Vignettes 571 (3%)

Code characteristics

Cyclomatic complexity: 5.0 median / 58 max
Test cases: 212 / 0.45 per code line

Test coverage

Line coverage

59%

Expression

57.5%

Tests / Examples

59.0% / – ex

Functions

120 37 exported

Complexity

8.3 avg / 58 max

Call network

120 nodes / 185 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

120 functions

Function	Cyclo	Coverage
create_gradient_colors exp	4	0%
create_legend_theme exp	7	0%
create_pathway_class_theme exp	1	0%
format_pvalue_smart exp	6	0%
get_available_themes exp	1	0%
get_significance_colors exp	3	0%

Datasets

Bundled datasets · 10

Name	Class	Rows × Cols	Also ships in
daa_annotated_results_df	data.frame	13 × 11	–
daa_results_df	data.frame	194 × 7	–
ec_reference	data.frame	8,405 × 2	–
kegg_abundance	data.frame	194 × 50	–
kegg_pathway_reference	data.frame	505 × 2	–
ko_reference	data.frame	58,693 × 5	–
ko_to_go_reference	tbl_df/tbl/data.frame	381 × 4	–
ko_to_kegg_reference	tbl_df/tbl/data.frame	63,810 × 9	–
metacyc_reference	data.frame	2,714 × 2	–
metacyc_to_ec_reference	data.frame	575 × 2	–

People & History

People (2)

Maintainer (1)

Chen Yang

Author, Maintainer

Authors (2)

Chen Yang

Author, Maintainer

Liangliang Zhang

Author

Package Timeline

19 releases. Pick two to compare their code metrics. R releases are shown for context.

2.5.17Latest
2026-06-05 · current release · diff ↗
2.5.16
2026-05-20 · diff ↗
2.5.14
2026-04-30 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.5.12
2026-04-10 · diff ↗
2.5.10
2026-02-12 · diff ↗
2.5.2
2025-08-26 · diff ↗
2.3.2
2025-07-16 · diff ↗
2.1.2
2025-04-13 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.0
2025-04-03 · diff ↗
unarchivedReturned to CRAN
2025-04-03
archivedRemoved from CRAN
2024-11-25
issues were not corrected in time Requires BioC packages no longer available as of BioC 3.20
R
R 4.4.0 released · 2024-04-24
1.7.3
2023-11-08 · diff ↗
unarchivedReturned to CRAN
2023-11-08

Show 12 earlier events

archivedRemoved from CRAN
2023-11-01
check problems were not corrected in time
1.7.2
2023-08-13 · diff ↗
1.7.1
2023-06-09 · diff ↗
1.7.0
2023-05-31 · diff ↗
1.6.5
2023-05-13 · diff ↗
1.6.3
2023-05-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6.0
2023-04-08 · diff ↗
1.5.0
2023-04-04 · diff ↗
1.4.9
2023-03-28 · diff ↗
1.4.8
2023-03-24
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-24
Total releases: 19 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.7 MB / 13 files
Download size: 3.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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