plot.GeNetClassifierReturn: Plot GeNetClassifierReturn

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

Description

Allows generating the plots from the objet created by geNetClassifier.

Usage

## S3 method for class 'GeNetClassifierReturn'
plot(x, y="missing", fileName = NULL, lpThreshold = 0.95, 
    numGenesLpPlot = 1000, numGenesNetworkPlot = 100, 
    geneLabels = NULL, verbose = TRUE, ...)

Arguments

x	GeNetClassifierReturn. Object returned by the main function "geNetClassifier".
fileName	Character. File name to save the plots.
lpThreshold	Numeric between 0 and 1. Required posterior probability value to consider a gene 'significant'.
numGenesLpPlot	Integer. Number of genes to show in the significant genes plot.
numGenesNetworkPlot	Integer. Number of genes (nodes) to plot in the network.
geneLabels	Vector or Matrix. Gene name, ID or label which should be shown in the returned results and plots.
verbose	Logical. If TRUE, messages indicating the execution progress will be printed on screen.
y	Not required.
...	Not required

Details

The plots are generated by default by geNetClassifier. This function allows re-plotting them with different parameters.

Value

Plots (depending on the available info):
- Significant genes
- Classification genes' Discriminant Power
- Top ranked genes network (for each class)

See Also

Main package function and classifier training: geNetClassifier
Class GeNetClassifierReturn
Other plotting functions:
- plotDiscriminantPower
- plot.GenesRanking
- plotNetwork

Examples

# Train or load an already trained classifier
data(leukemiasClassifier)

# Plot default plots on-screen 
plot(leukemiasClassifier)

# Save plots on file 
# (includes Discriminant Power of all genes, but the networks will not be interactive)
plot(leukemiasClassifier, fileName="newPlots")

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