ReorderCluster (version 2.0)

RearrangeData: Sample function to perform optimal reordering of the hierarchical tree according to class labels

Description

Provides the main scheme to perform optimal reordering of the hierarchical tree according to class labels for any dataset

Usage

RearrangeData(matr,class,clustering.method="complete",cDend=FALSE,dirpath="",cpp=TRUE)

Arguments

matr

a dataset, a matrix of feature values for several cases.

class

a character vector or numeric vector, containing the class labels of the dataset objects

clustering.method

a method for performing the hierarchical clustering. The method names corresponds to the methods, that are used for the hclust function. The default value is "complete".

cDend

A binary variable with values TRUE/FALSE enables or desable the visualiztion of the color dendrogram. Default is FALSE.

dirpath

A path to the directory, where the heat map is saved. When the path is empry (default) the heat map is visualized on the display.

cpp

a binary variable, which allows to switch between dynamic programming algorithm, realized in R language OrderingJoseph and the same algorithm as the C++ function OrderingJosephC

Value

order

a numeric vector of the reordered leaves of the debdrogram.

A

a numerical nxn matrix, which stores the values of the evaluation function for the subtrees. Each cell (i,j) of the matrix A stores the best ordering (according to the evaluation function value) of the subtree starting with element i and ending with element j.

class

a vector of labels of the dataset objects, reordered according to the vector order.

Details

The function visualizes the heat map for the results of the hiererchical clustering of the input dataset, than the call to the function RearrangeJoseph enables the reordering of the dendrogram according to the supplied class labels. At the end the resultant dendrogram and the heat map are visualized.

References

Z. Bar-Joseph, D.K. Gifford, and T.S. Jaakkola. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics, 17:22-29, 2001.

See Also

RearrangeJoseph, OrderingJoseph

Examples

# NOT RUN {
data(leukemia)
rownames(leukemia)=leukemia[,1]
leukemia=leukemia[,-1]
matr=leukemia[,-101]
class=leukemia[,101]
matr=as.matrix(matr)
res=RearrangeData(matr,class)
# }