ClusterPlot: Colouring clusters in a dendrogram

In IntClust: Integration of Multiple Data Sets with Clustering Techniques

Description

Plot a dendrogram with leaves colored by a result of choice.

Usage

ClusterPlot(Data1, Data2 = NULL, nrclusters = NULL, cols = NULL,
  colorComps = NULL, hangdend = 0.02, plottype = "new", location = NULL,
  ...)

Arguments

Data1	The resulting clustering of a method which contains the dendrogram to be colored.
Data2	Optional. The resulting clustering of another method , i.e. the resulting clustering on which the colors should be based. Default is NULL.
nrclusters	Optional. The number of clusters to cut the dendrogram in. If not specified the dendrogram will be drawn without colours to discern the different clusters. Default is NULL.
cols	The colours for the clusters if nrclusters is specified. Default is NULL.
colorComps	If only a specific set of objects needs to be highlighted, this can be specified here. The objects should be given in a character vector. If specified, all other compound labels will be colored black. Default is NULL.
hangdend	A specification for the length of the brances of the dendrogram. Default is 0.02.
plottype	Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document. Default is "new".
location	If plottype is "pdf", a location should be provided in "location" and the figure is saved there. Default is NULL.
...	Other options which can be given to the plot function.

Value

A plot of the dendrogram of the first clustering result with colored leaves. If a second clustering result is given in Data2, the colors are based on this clustering result.

Examples

## Not run: 
data(fingerprintMat)
data(targetMat)
data(Colors1)

MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)

ClusterPlot(MCF7_T ,nrclusters=7,cols=Colors1,plottype="new",location=NULL,
main="Clustering on Target Predictions: Dendrogram",ylim=c(-0.1,1.8))

## End(Not run)

Example output

IntClust documentation built on May 2, 2019, 5:51 a.m.