u12Boxplot: U12 boxplot

Description Usage Arguments Value Author(s) See Also Examples

View source: R/u12Boxplot.R

Description

A boxplot method for U12 and U2-type introns of SummarizedExperiment objects.

Usage

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u12Boxplot(x, sampleAnnoCol=NA, intExCol="int_ex",
	intTypeCol="int_type", intronExon, col="white",
	boxplotNames=c(), lasNames=3, outline=FALSE, addGrid=FALSE, ...)

Arguments

x

Object of type SummarizedExperiment.

sampleAnnoCol

Which colummn of colData in x to consider for plotting.

intExCol

Column name (or number) that represents whether each row of x assays is "intron" or "exon".

intTypeCol

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

intronExon

Whether plot intron retention (set intronExon="intron") or exon-exon junction (set intronExon="exon") levels.

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 U12/U2 (intron annotation) 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() function.

Value

A SummarizedExperiment object.

Author(s)

Ali Oghabian

See Also

u12BoxplotNb

Examples

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u12Boxplot(mdsChr22Obj, sampleAnnoCol="type", 
    intExCol="int_ex",  intTypeCol="intron_type", intronExon="intron", 
    col=rep(c("orange", "yellow"),3) ,  lasNames=3, 
    outline=FALSE, ylab="FPKM", cex.axis=0.8)

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.