densityClust (version 0.3.3)

densityClust-package: Clustering by fast search and find of density peaks

Description

This package implement the clustering algorithm described by Alex Rodriguez and Alessandro Laio (2014). It provides the user with tools for generating the initial rho and delta values for each observation as well as using these to assign observations to clusters. This is done in two passes so the user is free to reassign observations to clusters using a new set of rho and delta thresholds, without needing to recalculate everything.

Plotting

Two types of plots are supported by this package, and both mimics the types of plots used in the publication for the algorithm. The standard plot function produces a decision plot, with optional colouring of cluster peaks if these are assigned. Furthermore plotMDS() performs a multidimensional scaling of the distance matrix and plots this as a scatterplot. If clusters are assigned observations are coloured according to their assignment.

Cluster detection

The two main functions for this package are densityClust() and findClusters(). The former takes a distance matrix and optionally a distance cutoff and calculates rho and delta for each observation. The latter takes the output of densityClust() and make cluster assignment for each observation based on a user defined rho and delta threshold. If the thresholds are not specified the user is able to supply them interactively by clicking on a decision plot.

Author

Maintainer: Thomas Lin Pedersen

Authors:

• Sean Hughes

• Xiaojie Qiu

References

Rodriguez, A., & Laio, A. (2014). Clustering by fast search and find of density peaks. Science, 344(6191), 1492-1496. doi:10.1126/science.1242072

See Also

densityClust(), findClusters(), plotMDS()

Examples

irisDist <- dist(iris[,1:4])
irisClust <- densityClust(irisDist, gaussian=TRUE)
plot(irisClust) # Inspect clustering attributes to define thresholds

irisClust <- findClusters(irisClust, rho=2, delta=2)
plotMDS(irisClust)
split(iris[,5], irisClust$clusters)