Plot observations using t-distributed neighbor embedding and colour by cluster

Description

This function produces an t-SNE scatterplot based on the distance matrix of the densityCluster object (if there is only the coordinates information, a distance matrix will be calculate first), and, if clusters are defined, colours each observation according to cluster affiliation. Observations belonging to a cluster core is plotted with filled circles and observations belonging to the halo with hollow circles.

Usage

plotTSNE(x, ...)

Arguments

See Also

densityClust() for creating densityCluster objects, and plotMDS() for an alternative plotting approach.

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)
plotTSNE(irisClust)
split(iris[,5], irisClust$clusters)