u12Boxplot: U12 boxplot
In IntEREst: Intron-Exon Retention Estimator

Description Usage Arguments Value Author(s) See Also Examples

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

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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, ...)

`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.

A SummarizedExperiment object.

Ali Oghabian

u12BoxplotNb

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)