clustComp

DOI: 10.18129/B9.bioc.clustComp    

Clustering Comparison Package

Bioconductor version: Release (3.11)

clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.

Author: Aurora Torrente and Alvis Brazma.

Maintainer: Aurora Torrente <aurora at ebi.ac.uk>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clustComp")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("clustComp")

 

PDF	R Script	The clustComp Package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneExpression, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.3 (R-3.3) (4.5 years)
License	GPL (>= 2)
Depends	R (>= 3.3)
Imports	sm, stats, graphics, grDevices
LinkingTo
Suggests	Biobase, colonCA, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	clustComp_1.16.0.tar.gz
Windows Binary	clustComp_1.16.0.zip
macOS 10.13 (High Sierra)	clustComp_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/clustComp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clustComp
Package Short Url	https://bioconductor.org/packages/clustComp/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive