plotNetwork: Plot GenesNetwork

Description

Plots the coexpression and/or mutual information network for the given genes.

Usage

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)

Arguments

genesNetwork

List of GenesNetwork returned by geNetClassifier. (@genesNetwork)

classificationGenes

Matrix or classificationGenes returned by geNetClassifier. (@classificationGenes)

genesRanking

Matrix or genesRanking returned by geNetClassifier. (@genesRanking)

genesInfo

List or data.frame with the properties of the genes to plot: genesDetails(_@genesRanking)

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 invisible), assign it to a variable if needed.

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.

Value

Graph list: List with the plotted igraph objects.
Network plots: Shown throught the standard output devide or saved in the working directory as 'fileName.pdf' if fileName was provided.

References

Main package function and classifier training: geNetClassifier

Package igraph

Examples

Run this code


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")