idiogramFISH

2.0.13

Shiny App. Idiograms with Marks and Karyotype Indices

0packages depend

10.3Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Fernando RoaFirst published 2019-08-2432 releasesCRAN page ↗GitLab ↗

Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) doi:10.1111/j.1601-5223.1964.tb01953.x, karyotype indices of Watanabe et al. (1999) doi:10.1007/PL00013869 and Romero-Zarco (1986) doi:10.2307/1221906 and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).

Install

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

install.packages("idiogramFISH", 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("ferroao/idiogramFISH")

Development version from ferroao/idiogramFISH. 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-idiogramfish

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-idiogramFISH

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-idiogramFISH

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 5.3 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,930 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 15%

Downloads

10.3K

CRAN downloads in the past year

Rank #4,202 · ~28/day · ~861/mo

Releases R versions

Daily download trend is not available in this view yet.

35530 days

2.1K90 days

10.3K1 year

Compare downloads with other packages →

Also on123 r2u10 autocran

Repository

GitLab ↗ ferroao/idiogramfish

Repository practices

Upstream repositoryBeta

Repository gitlab.com/ferroao/idiogramfish is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (6)

rlang crayon plyr dplyr tidyr scales

LinkingTo (0)

none

Suggests (20)

rentrez ggplot2 ggpubr ggtree phytools treeio rmdformats knitr kableExtra rvcheck badger rmarkdown RCurl shiny shinydashboard rhandsontable gtools rclipboard clipr shinyjs

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Fernando Roa

Author, Maintainer

Authors (1)

Fernando Roa

Author, Maintainer

Contributors (1)

Mariana PC Telles

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.13Latest
2023-08-22 · current release · diff ↗
2.0.12
2023-06-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.11
2023-04-11 · diff ↗
2.0.10
2023-04-05 · diff ↗
2.0.9
2022-09-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.0.8
2022-01-11 · diff ↗
2.0.6
2021-09-30 · diff ↗
2.0.5
2021-05-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.4
2021-04-25 · diff ↗
2.0.3
2021-04-13 · diff ↗

Show 24 earlier events

2.0.2
2021-03-04 · diff ↗
2.0.0
2021-02-06 · diff ↗
1.16.8
2020-12-01 · diff ↗
1.16.7
2020-10-15 · diff ↗
1.16.6
2020-09-17 · diff ↗
1.16.1
2020-07-30 · diff ↗
1.15.3
2020-07-02 · diff ↗
1.15.1
2020-06-03 · diff ↗
1.14.11
2020-05-01 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.14.7
2020-03-28 · diff ↗
1.14.2
2020-02-27 · diff ↗
1.12.1
2020-01-10 · diff ↗
1.11.1
2019-12-12 · diff ↗
1.9.1
2019-11-29 · diff ↗
1.8.3
2019-11-14 · diff ↗
1.8.1
2019-10-29 · diff ↗
1.7.1
2019-10-20 · diff ↗
1.6.3
2019-10-13 · diff ↗
1.6.1
2019-10-04 · diff ↗
1.5.1
2019-09-27 · diff ↗
1.2.1
2019-09-17 · diff ↗
1.0.0
2019-08-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-24
Total releases: 32 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5
Bundled data: 14 KB / 27 files
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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