boxplot: Box plots

In BiocGenerics: S4 generic functions used in Bioconductor

Description

Produce box-and-whisker plot(s) of the given (grouped) values.

NOTE: This man page is for the boxplot S4 generic function defined in the BiocGenerics package. See ?graphics::boxplot for the default method (defined in the graphics package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

boxplot(x, ...)

Arguments

x, ...

See ?graphics::boxplot.

Value

See ?graphics::boxplot for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• graphics::boxplot for the default boxplot method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• boxplot,AffyBatch-method in the affy package for an example of a specific boxplot method (defined for AffyBatch objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

boxplot
showMethods("boxplot")
selectMethod("boxplot", "ANY")  # the default method

library(affy)
showMethods("boxplot")
## The boxplot() method for AffyBatch objects:
selectMethod("boxplot", "AffyBatch")

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

standardGeneric for "boxplot" defined from package "graphics"

function (x, ...) 
standardGeneric("boxplot")
<environment: 0x5607826b3408>
Methods may be defined for arguments: x
Use  showMethods("boxplot")  for currently available ones.
Function: boxplot (package graphics)
x="ANY"

Method Definition (Class "derivedDefaultMethod"):

function (x, ...) 
UseMethod("boxplot")
<bytecode: 0x5607826eb570>
<environment: namespace:graphics>

Signatures:
        x    
target  "ANY"
defined "ANY"
Loading required package: Biobase
Welcome to Bioconductor

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

Function: boxplot (package graphics)
x="AffyBatch"
x="ANY"

Method Definition:

function (x, ...) 
{
    .local <- function (x, which = "both", range = 0, main, ...) 
    {
        tmp <- description(x)
        if (missing(main) && (is(tmp, "MIAME"))) 
            main <- tmp@title
        tmp <- unlist(indexProbes(x, which))
        tmp <- tmp[seq(1, length(tmp), len = 5000)]
        boxplot(data.frame(log2(intensity(x)[tmp, ])), main = main, 
            range = range, ...)
    }
    .local(x, ...)
}
<bytecode: 0x56078105c470>
<environment: namespace:affy>

Signatures:
        x          
target  "AffyBatch"
defined "AffyBatch"

BiocGenerics documentation built on April 17, 2021, 6:01 p.m.