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.

Install the latest version of this package by entering the following in R:

```
source("https://bioconductor.org/biocLite.R")
biocLite("clustComp")
```

Author | Aurora Torrente and Alvis Brazma. |

Bioconductor views | Clustering GeneExpression Visualization |

Date of publication | None |

Maintainer | Aurora Torrente <aurora@ebi.ac.uk> |

License | GPL (>= 2) |

Version | 1.4.0 |

**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...

DESCRIPTION

NAMESPACE

R

R/SCmapping.R
R/barycentre.R
R/drawTreeGraph.R
R/dyn.cross.R
R/flatVSflat.R
R/flatVShier.R
R/insert.R
R/score.crossing.R
R/score.it.R
build

build/vignette.rds

inst

inst/NEWS

inst/doc

inst/doc/clustComp.R
inst/doc/clustComp.Rnw

inst/doc/clustComp.pdf

inst/unitTests

inst/unitTests/test_barycentre.R
inst/unitTests/test_dyn.cross.R
inst/unitTests/test_insert.R
man

man/SCmapping.Rd
man/barycentre.Rd
man/drawTreeGraph.Rd
man/dyn.cross.Rd
man/flatVSflat.Rd
man/flatVShier.Rd
man/insert.Rd
man/score.crossing.Rd
man/score.it.Rd
tests

tests/runTests.R
vignettes

vignettes/clustComp.Rnw

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

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