u12Boxplot: U12 boxplot

In gacatag/IntEREst: Intron-Exon Retention Estimator

U12 boxplot

Description

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

Usage

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

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)

gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.