u12Boxplot {IntEREst} | R Documentation

## 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)

[Package IntEREst version 1.2.2 Index]