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]