plot.GeNetClassifierReturn {geNetClassifier} | R Documentation

## 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

### 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")

[Package geNetClassifier version 1.27.9 Index]