DetermineWeight_SilClust: Determines an optimal weight for weighted clustering by...
In IntClust: Integration of Multiple Data Sets with Clustering Techniques

Description Usage Arguments Details Value Examples

The function DetermineWeight_SilClust determines an optimal weight for weighted similarity clustering by calculating silhouettes widths. See "Details" for a more elaborate description.

DetermineWeight_SilClust(List, type = c("data", "dist", "clusters"),
  distmeasure = c("tanimoto", "tanimoto"), normalize = c(FALSE, FALSE),
  method = c(NULL, NULL), weight = seq(0, 1, by = 0.01),
  nrclusters = NULL, names = NULL, nboot = 10, StopRange = FALSE,
  plottype = "new", location = NULL)

`List`	A list of matrices of the same type. It is assumed the rows are corresponding with the objects.
`type`	indicates whether the provided matrices in "List" are either data matrices, distance matrices or clustering results obtained from the data. If type="dist" the calculation of the distance matrices is skipped and if type="clusters" the single source clustering is skipped. Type should be one of "data", "dist" or "clusters".
`distmeasure`	A vector of the distance measures to be used on each data matrix. Should be one of "tanimoto", "euclidean", "jaccard", "hamming". Defaults to c("tanimoto","tanimoto").
`normalize`	Logical. Indicates whether to normalize the distance matrices or not, defaults to c(FALSE, FALSE) for two data sets. This is recommended if different distance types are used. More details on normalization in `Normalization`.
`method`	A method of normalization. Should be one of "Quantile","Fisher-Yates", "standardize","Range" or any of the first letters of these names. Default is c(NULL,NULL) for two data sets.
`weight`	Optional. A list of different weight combinations for the data sets in List. If NULL, the weights are determined to be equal for each data set. It is further possible to fix weights for some data matrices and to let it vary randomly for the remaining data sets. Defaults to seq(1,0,-0.1). An example is provided in the details.
`nrclusters`	The number of clusters to cut the dendrogram in. This is necessary for the computation of the Jaccard coefficient. Default is NULL.
`names`	The labels to give to the elements in List. Default is NULL.
`nboot`	Number of bootstraps to be run. Default is 10.
`StopRange`	Logical. Indicates whether the distance matrices with values not between zero and one should be standardized to have so. If FALSE the range normalization is performed. See `Normalization`. If TRUE, the distance matrices are not changed. This is recommended if different types of data are used such that these are comparable. Default is FALSE.
`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. Default is "new".
`location`	If plottype is "pdf", a location should be provided in "location" and the figure is saved there. Default is FALSE.

For each given weight, a linear combination of the distance matrices of the single data sources is obtained. For these distance matrices, medoid clustering with nrclusters is set up by the pam function of the cluster and the silhouette widths are retrieved. These widths indicates how well an object fits in its current cluster. Values around one indicate an appropriate cluster. The silhouette widths are regressed in function of the cluster membership determined by the objects. First, in function of the cluster membership determined by the weighted combination. Then, also in function of the cluster membership determined by the single source clustering. The regression function is fit by the lm function and the r.squared value is retrieved. Ther.squared value indicates how much of the variance of the silhouette widths is explained by the membership. Optimally this value is high.

Next, a statistic is determined. Suppose that RWW is the r.squared retrieved from regressing the weighted silhouette widths versus the weighted cluster membership and RWX the r.squared retrieved from regressing the weighted silhouette widths versus the cluster membership determined by data X. If M is total number of data sources, than statistic is obtained as:

Stat=abs(M*RWW-∑{RWX})

The lower the statistical value, the better the weighted clustering is explained by the single data sources. The goal is to obtain the weights for which this value is minimized. Via bootstrapping a p-value is obtained for every statistic.

The weight combinations should be provided as elements in a list. For three data matrices an example could be: weights=list(c(0.5,0.2,0.3),c(0.1,0.5,0.4)). To provide a fixed weight for some data sets and let it vary randomly for others, the element "x" indicates a free parameter. An example is weights=list(c(0.7,"x","x")). The weight 0.7 is now fixed for the first data matrix while the remaining 0.3 weight will be divided over the other two data sets. This implies that every combination of the sequence from 0 to 0.3 with steps of 0.1 will be reported and clustering will be performed for each.

Two plots are made: one of the statistical values versus the weights and one of the p-values versus the weights. Further, a list with two elements is returned:

`Result`	A data frame with the statistic for each weight combination
`Weight`	The optimal weight

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

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

L=list(MCF7_F,MCF7_T)

MC7_Weight=DetermineWeight_SilClust(List=L,type="clusters",distmeasure=
c("tanimoto","tanimoto"),normalize=c(FALSE,FALSE),method=c(NULL,NULL),
weight=seq(0,1,by=0.01),nrclusters=c(7,7),names=c("FP","TP"),nboot=10,
StopRange=FALSE,plottype="new",location=NULL)

## End(Not run)