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

In IntClust: Integrated Data Analysis via 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.

Details

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

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.

Author(s)

Marijke Van Moerbeke

See Also

ComparePlot

Examples

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)

IntClust documentation built on May 2, 2019, 5:23 p.m.