CompareInteractive: Interactive comparison of clustering results for a specific cluster or method.

Description

A visual comparison of all methods is handy to see which compounds will always cluster together independent of the applied methods. The function CompareInteractive plots the comparison over the specified methods. A cluster or method can than be identified by clicking and is plotted separately against the single source or other specified methods.

Usage

CompareInteractive(ListM,ListS,nrclusters=NULL,cols=NULL,fusionsLogM
=FALSE,fusionsLogS=FALSE,WeightClustM=FALSE,WeightClustS=FALSE,
namesM=NULL,namesS=NULL,marginsM=c(2,2.5,2,2.5),marginsS=c(8,2.5,2,2.5)
,Interactive=TRUE,N=1,...)

Arguments

ListM

A list of the multiple source clustering or other methods to be compared and from which a cluster or method will be identified. The first element of the list will be used as the reference in ReorderToReference.

ListS

A list of the single source clustering or other methods the identified result will be compared to. The first element of the list will be used as the reference in ReorderToReference.

nrclusters

The number of clusters to cut the dendrogram in.

cols

The hex codes of the colors to be used.

fusionsLogM

The fusionsLog parameter for the elements in ListM. To be handed to ReorderToReference.

fusionsLogS

The fusionslog parameter for the elements in ListS. To be handed to ReorderToReference.

WeightClustM

The WeightClust parameter for the elements in ListM. To be handed to ReorderToReference.

WeightClustS

The WeightClust parameter for the elements in ListS. To be handed to ReorderToReference.

namesS

Optional. Names of the single source clusterings to be used as labels for the columns.

namesM

Optional. Names of the multiple source clusterings to be used as labels for the columns.

marginsM

Optional. Margins to be used for the plot for the elements is ListM after the identification.

marginsS

Optional. Margins to be used for the plot for the elements is ListS after the identification.

Interactive

Optional. Do you want an interactive plot? Defaults to TRUE, if not the function provides the same as ComparePlot for the elements in ListM.

The number of methods/clusters you want to identify.

…

Other options which can be given to the color2D.matplot function.

Value

The returned value is a plot of the comparison of the elements of ListM. On this plot multiple clusters and/or methods can be identified. Click on a cluster of a specific method to see how that cluster of that method compares to the elements in ListS. Click left next to a row to identify a all cluster of a specific method. A new plotting window will appear for every identification.

Details

This function relies on ComparePlot to plot the results.

Examples

Run this code

# NOT RUN {
data(fingerprintMat)
data(targetMat)
data(Colors2)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)

L=list(fingerprintMat,targetMat)

MCF7_W=WeightedClust(L,type="data",distmeasure=c("tanimoto","tanimoto"),normalize=FALSE,
method=NULL,weight=seq(1,0,-0.1),WeightClust=0.5,clust="agnes",linkage="ward",StopRange=FALSE)

ListM=list(MCF7_W)
namesM=c(seq(1.0,0.0,-0.1))

ListS=list(MCF7_F,MCF7_T)
namesS=c("FP","TP")

CompareInteractive(ListM,ListS,nrclusters=7,cols=Colors2,fusionsLogM=FALSE,
fusionsLogS=FALSE,WeightClustM=FALSE,WeightClustS=TRUE,namesM,namesS,
marginsM=c(2,2.5,2,2.5),marginsS=c(8,2.5,2,2.5),Interactive=TRUE,N=1)
# }