boxplot-method: boxplot - method

Description Usage Arguments Value Author(s) See Also Examples

Description

boxplot method for SummarizedExperiment objects.

Usage

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## S4 method for signature 'SummarizedExperiment'
boxplot(x, sampleAnnoCol=NA, 
	intexTypeCol="int_type", intexType=c(), col="white", boxplotNames=c(), 
	lasNames=3, outline=FALSE, addGrid=FALSE, ...)

Arguments

x

Object of type SummarizedExperiment generated by either interest(), interest.sequential() or readInterestResults().

sampleAnnoCol

Which colummn of colData in x to consider for plotting.

intexTypeCol

Column name (or number) that represents what type of intron/exon each row of x assays represents.

intexType

A vector of characters describing types of introns/exons to be plotted. They must be elements in the intexTypeCol column of the rowData of x. rowData of x is a dataframe that includes various annotations of the introns/exons.

col

Vector showing box colours. It is either of size 1 or the same size as the number of groups to be plotted.

boxplotNames

Names to write under boxes. If not defined, as names, it pastes the row (intron/exon) annotation names to the sample group annotations separated by a space " ".

lasNames

Orientation of the box names.

outline

If outline is TRUE the outlier points are drawn otherwise if FALSE (default) they are not.

addGrid

Whether add a grid under the boxplots (FALSE by default).

...

Other arguments to pass to the boxplot() and axis function.

Value

Returns NULL.

Author(s)

Ali Oghabian

See Also

Class: SummarizedExperiment-class Method: counts-method plot-method

Examples

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#Plotting U12- vs U2-type introns
par(mar=c(8,4,2,1))
boxplot(x=mdsChr22Obj, sampleAnnoCol="type", intexTypeCol="intron_type", 
	intexType=c("U2", "U12"), 
	col=rep(c("yellow", "orange"),3), 
	boxplotNames=c(), lasNames=3, outline=FALSE, 
	addGrid=TRUE)

IntEREst documentation built on Feb. 11, 2018, 3:09 p.m.