boxplot: Box plots

Description Usage Arguments Value See Also Examples

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

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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

Examples

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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:BiocGenericsThe following objects are masked frompackage:parallel:

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

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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.