NGCHM

1.0.4

Next Generation Clustered Heat Maps

0packages depend

7.8Kdownloads / year

13.4%test coverage

11/13checks pass

Overview

About

Maintained by Mary A RohrdanzFirst published 2024-01-164 releasesCRAN page ↗GitHub ↗

Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) doi:10.12688/f1000research.20590.2 for more details.

Install

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

install.packages("NGCHM", 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("MD-Anderson-Bioinformatics/NGCHM-R")

Development version from MD-Anderson-Bioinformatics/NGCHM-R. 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-ngchm

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-NGCHM

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-NGCHM

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

13.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 35 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

7.8K

CRAN downloads in the past year

Rank #5,785 · ~21/day · ~652/mo

Releases R versions

Daily download trend is not available in this view yet.

37130 days

1.7K90 days

7.8K1 year

Compare downloads with other packages →

Also on86 r2u29 autocran

Repository

GitHub ↗ md-anderson-bioinformatics/ngchm-r

9Stars

2Forks

18Open issues

0Open PRs

4Releases

479Commits

5Contributors

ng-chmheatmapnci-itcr

479 commits · Last activity 2026-05-04

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/md-anderson-bioinformatics/ngchm-r on 2026-07-19.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

digestgrDeviceshtmltools httr jsonlite logger (>= 0.2.0)methodsstatstsvioutils

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown Rtsne testthat umap uwot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 10,962 (66%)Rd 5,665 (34%)

Code characteristics

Object systems

S316S4 class32S4 generic40S4 method107

Cyclomatic complexity: 3.0 median / 39 max
Test cases: 4 / 0.00 per code line
System requirements: 1 external

Test coverage

Line coverage

13%

Expression

12.6%

Tests / Examples

13.4% / 18% ex

Functions

262 106 exported

Complexity

5.2 avg / 39 max

Call network

262 nodes / 360 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

262 functions

Function	Cyclo	Coverage
chmAddPCA exp	14	0%
chmAddReducedDim exp	15	0%
chmAddTSNE exp	7	0%
chmAddUMAP exp	6	0%
chmAddUWOT exp	7	0%
chmAxis exp	1	0%

People & History

People (5)

Maintainer (1)

Mary A Rohrdanz

Contributor, Maintainer

Authors (1)

Bradley M Broom

Author

Contributors (3)

Mary A Rohrdanz

Contributor, Maintainer

James M Melott

Contributor

Chris Wakefield

Contributor

MD Anderson Cancer Center

Listed in earlier versions (4)

Mary A

no longer listed · 1.0.1 to 1.0.4

Bradley M

no longer listed · 1.0.1 to 1.0.4

James Melott

no longer listed · 1.0.1 to 1.0.3

James M

no longer listed · 1.0.4

Package Timeline

4 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
1.0.4Latest
2024-12-17 · current release · diff ↗
1.0.3
2024-05-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.2
2024-03-28 · diff ↗
1.0.1
2024-01-16
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-16
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Additional repositories: md-anderson-bioinformatics.r-universe.dev
Minimum R: ≥ 3.5.0
Download size: 142 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →