CytoMDS
Bioc currentLow Dimensions projection of cytometry samples
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 25 exported
Complexity
7.5 avg / 56 max
Call network
38 nodes / 35 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
9,191
Files
82
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
25
Internal functions
13
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
2.84
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
175 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (1)
Bioconductor (1)
People
- Philippe Hauchamps author maintainer
- Laurent Gatto author
- Dan Lin contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CytoMDS")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.
From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.