plotNetwork {geNetClassifier} | R Documentation |
Plots the coexpression and/or mutual information network for the given genes.
plotNetwork(genesNetwork, classificationGenes=NULL, genesRanking=NULL, genesInfo=NULL, geneLabels=NULL, returniGraphs=FALSE, plotType="dynamic", fileName=NULL, plotAllNodesNetwork=TRUE, plotOnlyConnectedNodesNetwork=FALSE, plotClassifcationGenesNetwork=FALSE, labelSize=0.5, vertexSize=NULL, width=NULL, height=NULL, verbose=TRUE)
genesNetwork |
List of GenesNetwork returned by |
classificationGenes |
Matrix or classificationGenes returned by |
genesRanking |
Matrix or genesRanking returned by |
genesInfo |
List or data.frame with the properties of the genes to plot: |
geneLabels |
Vector or Matrix. Gene name, ID or label which should be shown in the returned results and plots. |
returniGraphs |
deprecated. A list with the plotted networks as igraph objects is always returned (see |
plotType |
Character. "dynamic": Interactive plot. "static": One canvas split for the different networks. "pdf": All the networks are saved into a pdf file. |
fileName |
Character. File name to save the plot with. If not provided, the plots will be shown through the standard output device. |
plotAllNodesNetwork |
Logical. If TRUE, plots a network only with all the available genes |
plotOnlyConnectedNodesNetwork |
Logical. If TRUE, plots a network only with the connected nodes/genes |
plotClassifcationGenesNetwork |
Logical. If TRUE, plots a network only with the classification genes |
labelSize |
Integer. Gene/node label size for static and pdf plots. |
vertexSize |
Integer. Vertex minimum size. |
width |
Numeric. Dinamic or pdf plot width. |
height |
Numeric. Dinamic or pdf plot height. |
verbose |
Logical. If TRUE, messages indicating the execution progress will be shown. |
Graph list |
List with the plotted |
Network plots |
Shown throught the standard output devide or saved in the working directory as 'fileName.pdf' if |
Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain
Main package function and classifier training:
geNetClassifier
Package igraph
plot.GenesNetwork()
is an alias to this function. It can allso be called as i.e. plotNetwork(clGenesSubNet$ALL)
Note: The slot @genesNetwork returned by geNetClassifier is a List of GenesNetworks!
data(leukemiasClassifier) # Step 1: Select a network or sub network # Sub-network containing only the classification genes: clGenesSubNet <- getSubNetwork(leukemiasClassifier@genesNetwork, leukemiasClassifier@classificationGenes) # Step 2: Select the details/info about the genes to plot # Classification genes' info: clGenesInfo <- genesDetails(leukemiasClassifier@classificationGenes) # Step 3: Plot the network # Network plots can be interactive or plotted as PDF file. # - - Use plotType="pdf" to save the network as a static pdf file. # This option is recommended for getting an overview of several networks. # - - To get an interactive network, just skip this argument. # Plot ALL network: plotNetwork(clGenesSubNet$ALL, genesInfo=clGenesInfo) # Plot AML network containing only the conected nodes: plotNetwork(clGenesSubNet$ALL, genesInfo=clGenesInfo, plotAllNodesNetwork=FALSE, plotOnlyConnectedNodesNetwork=TRUE) # The equivalent code to the plot geNetClassifier creates by default is: topRanking <- getTopRanking(leukemiasClassifier@genesRanking, numGenesClass=100) netTopGenes <- getSubNetwork(leukemiasClassifier@genesNetwork, getRanking(topRanking, showGeneID=TRUE)$geneID) plotNetwork(netTopGenes, classificationGenes=leukemiasClassifier@classificationGenes, genesRanking=topRanking, plotAllNodesNetwork=TRUE, plotOnlyConnectedNodesNetwork=TRUE, plotType="pdf", labelSize=0.3, fileName="leukemiasClassifier") # In order to save the network as text file, you can use: network2txt(leukemiasClassifier@genesNetwork, filePrefix="leukemiasNetwork")