clusterVisualHclust-class {goCluster}R Documentation

Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.

Description

This class can be used in order to visualize annotation terms that have been found as overrepresented in clusters identified with a hierarchical clustering. These annotation terms are displayed alongside the hierarchical clustering result.

Details

The class provides a wrapper around the prepareAxis-function. Please read the corresponding documentation for further details.

Slots

prepared:
Object of class "list", the number of vectors stored in this list corresponds to the number of annotations analyzed. Each vector contains the same number of items as there are nodes in the tree of the clustering (number of genes - 1). The order of appearence corresponds to the ordering of the dendrogram so that the sorted dendrogram and the annotation terms can be put alongside each other.

Additional slots are described in the documentation of the clusterVisual-class and clusterModule-class.

Extends

Class "clusterVisual", directly. Class "clusterModule", by class "clusterVisual".

Methods

config
signature(object = "clusterVisualHclust"): interactive setup of the class. There are no options that you can set on this class.
setup
signature(object = "clusterVisualHclust"): returns the configuration of the object as a list. Since there are no options to this class, this is always an empty list.
setup<-
signature(object = "clusterVisualHclust"): non-interactive setup of the class. Not necessary since this class has no options.
execute
signature(object = "clusterVisualHclust"): prepares the selected annotation terms for the visualization.
reset
signature(object = "clusterVisualHclust"): resets the results of this class so that the analysis can be run again.
display
signature(object = "clusterVisualHclust"): generates the actual graphic for this object.
print
signature(x = "clusterVisualHclust"): prints generic information about the object.

Author(s)

Gunnar Wrobel, http://www.gunnarwrobel.de.

See Also

prepareAxis, goCluster-class, clusterModule-class, clusterVisual-class

Examples


set.seed(1000)

data(benomylsetupsmall)

benomylsetupsmall$classalgo <- "clusterAlgorithmHclust"
benomylsetupsmall$algo$method   <- "complete"
benomylsetupsmall$algo$distance <- "euclidean"

benomylsetupsmall$classvisu <- "clusterVisualHclust"

a <- new("goCluster")

execute(a) <- benomylsetupsmall

if(interactive()){
## This example can only be run in an interactive mode

## This plot shows only one labeled region since the 
## loaded dataset has been reduced to only 100 genes. 
## Try the same with the full dataset
display(a, selection = 1)
}


[Package goCluster version 1.0.3 Index]