clustComp: Clustering Comparison Package

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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.
Date of publication
None
Maintainer
Aurora Torrente <aurora@ebi.ac.uk>
License
GPL (>= 2)
Version
1.2.2

View on Bioconductor

Man pages

barycentre
Computation of the barycentre-coordinate of a node connected...
drawTreeGraph
Plot the bi-graph determined by the branches in the tree and...
dyn.cross
Computation of the number of crossings in the bi-graph in a...
flatVSflat
Comparison of two flat clusterings
flatVShier
Comparison of a hierarchical and a flat clusterings
insert
Insert a set of values at a given position of a vector
SCmapping
Construction of the superclusters and the one-to-one mapping...
score.crossing
Computation of the aesthetics-based score of the parent and...
score.it
Computation of the information theoretic-based score of the...

Files in this package

clustComp/DESCRIPTION
clustComp/NAMESPACE
clustComp/R
clustComp/R/SCmapping.R
clustComp/R/barycentre.R
clustComp/R/drawTreeGraph.R
clustComp/R/dyn.cross.R
clustComp/R/flatVSflat.R
clustComp/R/flatVShier.R
clustComp/R/insert.R
clustComp/R/score.crossing.R
clustComp/R/score.it.R
clustComp/build
clustComp/build/vignette.rds
clustComp/inst
clustComp/inst/NEWS
clustComp/inst/doc
clustComp/inst/doc/clustComp.R
clustComp/inst/doc/clustComp.Rnw
clustComp/inst/doc/clustComp.pdf
clustComp/inst/unitTests
clustComp/inst/unitTests/test_barycentre.R
clustComp/inst/unitTests/test_dyn.cross.R
clustComp/inst/unitTests/test_insert.R
clustComp/man
clustComp/man/SCmapping.Rd
clustComp/man/barycentre.Rd
clustComp/man/drawTreeGraph.Rd
clustComp/man/dyn.cross.Rd
clustComp/man/flatVSflat.Rd
clustComp/man/flatVShier.Rd
clustComp/man/insert.Rd
clustComp/man/score.crossing.Rd
clustComp/man/score.it.Rd
clustComp/tests
clustComp/tests/runTests.R
clustComp/vignettes
clustComp/vignettes/clustComp.Rnw