clusterVisualization {transcriptogramer} | R Documentation |
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.
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)
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. |
RedeR package requirements: Java Runtime Environment (>= 6).
This function returns an object of the RedPort Class.
Diego Morais
differentiallyExpressed, transcriptogramPreprocess, GSE9988, GPL570, Hs900, association, transcriptogramStep1, transcriptogramStep2, RedPort
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)