plotNetwork: Plot GenesNetwork

In geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles

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.

Author(s)

Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain

References

Main package function and classifier training: geNetClassifier

Package igraph

See Also

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!

Examples

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")

geNetClassifier documentation built on Nov. 8, 2020, 4:53 p.m.