R: Sample function to perform optimal reordering of the...

RearrangeData {ReorderCluster} | R Documentation

## 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`

### 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.

### 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`.

### Author(s)

Natalia Novoselova,Frank Klawonn,Junxi wang

Maintainer: Natalia Novoselova <novos65@mail.ru>

### 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

    data(leukemia)
    rownames(leukemia)=leukemia[,1]
    leukemia=leukemia[,-1]
    matr=leukemia[,-101]
    class=leukemia[,101]
    matr=as.matrix(matr)
    res=RearrangeData(matr,class)

[Package ReorderCluster version 2.0 Index]