CompareSvsM: Comparison of clustering results for the single and multiple source clustering.

Description

A visual comparison of all methods is handy to see which compounds will always cluster together independent of the applied methods. The function CompareSvsM plots the ComparePlot of the single source clustering results on the left and that of the multiple source clustering results on the right such that a visual comparison is possible.

Usage

CompareSvsM(ListS,ListM, nrclusters = NULL, cols = NULL, fusionsLogS=FALSE,
fusionsLogM=FALSE,WeightClustS=FALSE,WeightClustM=FALSE, namesS = NULL,
namesM=NULL, margins = c(8.1, 3.1, 3.1, 4.1),plottype="new",location=NULL, ...)

Arguments

ListS

A list of the outputs from the single source clusterings to be compared. The first element of the list will be used as the reference in ReorderToReference.

ListM

A list of the outputs from the multiple source clusterings to be compared. The first element of the list will be used as the reference.

nrclusters

The number of clusters to cut the dendrogram in.

cols

The hex codes of the colors to be used.

fusionsLogS

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

fusionsLogM

The fusionsLog 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.

WeightClustM

The WeightClust parameter for the elements in ListM. 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.

margins

Optional. Margins to be used for the plot.

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, i.e. no new device is opened and the plot appears in the current device or document.

location

If plottype is "pdf", a location should be provided in "location" and the figure is saved there.

…

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

Value

The returned value is a plot with on the left the comparison over the objects in ListS and on the right a comparison over the objects in ListM.

Details

This function relies on ComparePlot to plot both the results of the single source clusterings as the multiple source clusterings.

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=seq(1.0,0.0,-0.1)

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

CompareSvsM(ListS,ListM,nrclusters=7,cols=Colors2,fusionsLogS=FALSE,
fusionsLogM=FALSE,WeightClustS=FALSE,WeightClustM=FALSE,namesS,
namesM,reverse=FALSE,plottype="new",location=NULL)
# }