IntClust (version 0.0.2)

TrackCluster: Follow a cluster over multiple methods

Description

It is often desired to track a specific selection of object over the different methods and/or weights. This can be done with the ClusterDistribution. For every method, it is tracked where the objects of the selections are situated.

Usage

TrackCluster(List, Selection, nrclusters=NULL, followMaxComps = FALSE, 
followClust = TRUE, fusionsLog = TRUE, WeightClust = TRUE, names = NULL
, SelectionPlot = TRUE, Table = TRUE, CompleteSelectionPlot = FALSE, 
ClusterPlot=FALSE,cols=NULL,legendposx=0.5,legendposy=2.4,plottype="new",location=NULL)

Arguments

List

A list of the clustering outputs.The first element of the list will be used as the reference in ReorderToReference.

Selection

The selection of objects to follow or a specific cluster number.

nrclusters

The number of clusters to cut the dendrogram in.

followMaxComps

Logical for plot. Whether to follow the maximum of objects.

followClust

Logical for plot. Whether to follow the specific cluster.

fusionsLog

To be handed to ReorderToReference.

WeightClust

To be handed to ReorderToReference.

names

Optional. Names of the methods.

SelectionPlot

Logical. Should a plot be produced. Depending on followMaxComps and followClust it focuses on the maximum of compounds or a cluster. It will not be indicated to which cluster compounds moved.

Table

Logical. Should a table with the compounds per method and the shared compounds be produced?

CompleteSelectionPlot

Logical. Should the complete distribution of the selection be plotted? This implies that it will be indicated to which cluster compounds will move.

ClusterPlot

Logical. Plot of specific cluster.

cols

The colors used for the different clusters.

legendposx

The x-coordinate of the legend on all plots.

legendposy

The y-coordinate of the legend on all plots.

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.

location

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

Value

The returned value is a list with an element for every method. This element is another list with the following elements:

Selection

The selection of compounds to follow

nr.clusters

the number of clusters the selection is divided over

nr.min.max.together

the minimum and maximum number of compounds found together

perc.min.max.together

minimum and maximum percentage of compounds found together

AllClusters

A list with an element per cluster that contains at least one of the compounds in Selection. The list contains the cluster number, the complete cluster, the objects that originally could be found in this cluster and which object were joined extra to it.

Depending on whether followMaxComps or followClust is specified, the cluster of interest is mentioned separately as well for easy access. If the option was specified to create a table, this can be found under the Table element. Each plot that was specified to be created is plotted in a new window in the graphics console.

Details

The result is provided with extra information as which compounds of the original selection can be found in this cluster and which are extra. Further, plots of the distribution of the compounds can be produced. One plot follows the complete distribution of the cluster while another one focuses on either the maximum number of compounds or a specific cluster, whatever is specified. It are the number of compounds that are plotted and the first element indicated the number of compounds in the selection. A table can be produced as well, that separates the objects that are shared over all methods from those extra in the original selection and extra for the other methods. The ReorderToReference is applied to make sure that the clusters are comparable over the methods.

The function is experimental and might not work in specific cases. Please let us know such that we can improve its functionality.

Examples

# NOT RUN {
data(fingerprintMat)
data(targetMat)
data(Colors1)

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(MCF7_F,MCF7_T)
names=c("FP","TP")

Comps=FindCluster(L,nrclusters=7,select=c(1,4))
Comps

CompsFPAll=TrackCluster(List=L,Selection=Comps,nrclusters=7,followMaxComps=TRUE,
followClust=FALSE,fusionsLog=TRUE,WeightClust=TRUE,names=names,SelectionPlot=TRUE,
Table=TRUE,CompleteSelectionPlot=TRUE,cols=Colors1,plottype="new")

# }