plot,biosign-method {biosigner} | R Documentation

## Plot method for 'biosign' signature objects

### Description

Displays classifier tiers or individual boxplots from selected features

### Usage

    ## S4 method for signature 'biosign'
    plot(x, y, tierMaxC = "S", typeC = c("tier",
      "boxplot")[1], file.pdfC = NULL, .sinkC = NULL, ...)

### Arguments

`x` | An S4 object of class `biosign`, created by the `biosign` function.
`y` | Currently not used.
`tierMaxC` | Character: Maximum level of tiers to display: Either 'S' and 'A', (for boxplot), or also 'B', 'C', 'D', and 'E' (for tiers) by decreasing number of selections
`typeC` | Character: Plot type; either 'tier' [default] displaying the comparison of signatures up to the selected 'tierMaxC' or 'boxplot' showing the individual boxplots of the features selected by all the classifiers
`file.pdfC` | Character: Figure filename ending with '.pdf'; default is NULL (no saving; displaying instead)
`.sinkC` | Character: Name of the file for R output diversion [default = NULL: no diversion]; Diversion of messages is required for the integration into Galaxy
`...` | Currently not used.

### Value

A plot is created on the current graphics device.

### Author(s)

Philippe Rinaudo and Etienne Thevenot (CEA)

### Examples

    ## loading the diaplasma dataset

    data(diaplasma)
    attach(diaplasma)

    ## restricting to a smaller dataset for this example

    featureSelVl <- variableMetadata[, "mzmed"] >= 490 & variableMetadata[, "mzmed"] < 500
    dataMatrix <- dataMatrix[, featureSelVl]
    variableMetadata <- variableMetadata[featureSelVl, ]

    ## signature selection for all 3 classifiers
    ## a bootI = 5 number of bootstraps is used for this example
    ## we recommend to keep the default bootI = 50 value for your analyzes

    set.seed(123)
    diaSign <- biosign(dataMatrix, sampleMetadata[, "type"], bootI = 5)

    ## individual boxplot of the selected signatures

    plot(diaSign, typeC = "boxplot")

    detach(diaplasma)

[Package biosigner version 1.8.0 Index]