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Last data update: 2014.03.03

R: Plot GeNetClassifierReturn

plot.GeNetClassifierReturn

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)

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(geNetClassifier)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: EBarrays
Loading required package: lattice
Loading required package: minet
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/geNetClassifier/plot.GeNetClassifierReturn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.GeNetClassifierReturn
> ### Title: Plot GeNetClassifierReturn
> ### Aliases: plotGeNetClassifierReturn
> ###   plotGeNetClassifierReturn,GeNetClassifierReturn-method
> ###   plot,GeNetClassifierReturn-method plot.GeNetClassifierReturn
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> 
> # Train or load an already trained classifier
> data(leukemiasClassifier)
> 
> # Plot default plots on-screen 
> plot(leukemiasClassifier)

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Warning message:
In plotDiscriminantPower(geNetClassifierReturn@classifier, classificationGenes = geNetClassifierReturn@classificationGenes,  :
  Up to 20 genes will be shown. To plot more genes specify a PDF output file name.
> 
> # Save plots on file 
> # (includes Discriminant Power of all genes, but the networks will not be interactive)
> plot(leukemiasClassifier, fileName="newPlots")
The plots were saved in /home/ddbj/DataUpdator-rgm3/target with the prefix 'newPlots'.
> 
> 
> 
> 
> 
> dev.off()
X11cairo 
       3 
>