R: Plot observations using t-distributed neighbor embedding and...

plotTSNE {densityClust} | R Documentation

## 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

`x` | A densityCluster object as produced by `densityClust()`
`...` | Additional parameters. Currently ignored

### 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)

[Package densityClust version 0.3 Index]