R Observatory: Metrics for ggmsa version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2021-08-17. Its history is shown below.

Reason: suggested packages not used conditionally

Details below reflect version 1.0.2, its last release before removal.

ggmsa

1.0.2

Plot Multiple Sequence Alignment using 'ggplot2'

1packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Guangchuang Yu6 releasesCRAN page ↗

Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.

Install

BioconductorR (source archive)Ubuntu (r2u)

BiocManager::install("ggmsa")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/ggmsa/ggmsa_1.0.2.tar.gz"
pkgFile <- "ggmsa_1.0.2.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0.2) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-ggmsa

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

14

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 89%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on279 r2u498 bioconda

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (14)

Biostrings ggplot2 magrittr tidyrutilsstatsstringr aplot RColorBrewer ggalt ggforcemethodsdplyr R4RNA

LinkingTo (0)

none

Suggests (12)

ggtreeExtra ggtree ape cowplot knitr prettydoc rmarkdown seqmagick readxl ggnewscale kableExtra gggenes

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

–indirect (not tracked)

ggaligner

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Guangchuang Yu

Author, Maintainer

Authors (2)

Guangchuang Yu

Author, Maintainer

Lang Zhou

Author

Contributors (2)

Shuangbin Xu

Contributor · added in 1.0.2

Huina Huang

Contributor

Package Timeline

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

R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2021-08-17
suggested packages not used conditionally
1.0.2
2021-08-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.0.6
2021-02-02 · diff ↗
0.0.5
2021-01-06 · diff ↗
0.0.4
2020-05-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.0.2
2020-01-08 · diff ↗
0.0.1
2019-10-07
R
R 3.6.0 released · 2019-04-26

Package metadata

Total releases: 6
License: Artistic-2.0 OSI
Minimum R: ≥ 3.5.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ggmsa")

Format

Yu, G., Zhou, L., Xu, S., & Huang, H. (n.d.). ggmsa: Plot Multiple Sequence Alignment using 'ggplot2' (Version 1.0.2) [Computer software]. Retrieved August 24, 2026, from https://CRAN.R-project.org/package=ggmsa

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ggmsa version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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