clusterVisualization {transcriptogramer} | R Documentation

## Displays graphs of the differentially expressed clusters

### Description

This method uses the RedeR package to display graphs of the differentially expressed clusters. If the DE slot has a column named Symbol, its contents will be used as node alias.

### Usage

    clusterVisualization(object, maincomp = FALSE, connected = FALSE,
      host = "127.0.0.1", port = 9091, clusters = NULL)

    ## S4 method for signature 'Transcriptogram'
    clusterVisualization(object, maincomp = FALSE,
      connected = FALSE, host = "127.0.0.1", port = 9091, clusters = NULL)

### Arguments

`object` | An object of class Transcriptogram.
`maincomp` | Logical value, set as TRUE if you want to display only the main component of each cluster, the default value of this argument is FALSE.
`connected` | Logical value, set as TRUE if you want to display only connected nodes, the default value of this argument is FALSE.
`host` | The domain name of the machine that is running the RedeR XML-RPC server.
`port` | An integer specifying the port on which the XML-RPC server should listen.
`clusters` | An integer vector specifying the clusters to be displayed, if NULL, all clusters will be displayed.

### Details

RedeR package requirements: Java Runtime Environment (>= 6).

### Value

This function returns an object of the RedPort Class.

### Author(s)

Diego Morais

### See Also

differentiallyExpressed, transcriptogramPreprocess, GSE9988, GPL570, Hs900, association, transcriptogramStep1, transcriptogramStep2, RedPort

### Examples

    transcriptogram <- transcriptogramPreprocess(association, Hs900, 50)
    ## Not run:
    transcriptogram <- transcriptogramStep1(transcriptogram, GSE9988, GPL570)
    transcriptogram <- transcriptogramStep2(transcriptogram)
    levels <- c(rep(FALSE, 3), rep(TRUE, 3))
    transcriptogram <- differentiallyExpressed(transcriptogram, levels, 0.01,
    DEsymbols)
    rdp <- clusterVisualization(transcriptogram)

    ## End(Not run)

[Package transcriptogramer version 1.2.1 Index]