geNetClassifier (version 1.12.0)

plot.GeNetClassifierReturn: Plot GeNetClassifierReturn

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

Value

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

Details

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

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")