u12BoxplotNb {IntEREst} | R Documentation

## boxplot U12 introns retention levels (or flanking exons junction levels) and (up/down)stream U2 introns (or exons junction levels)

### Description

boxplot U12 introns and (Up/Down)stream U2 introns in `SummarizedExperiment` objects.

### Usage

    u12BoxplotNb(x, sampleAnnoCol=2, intExCol="int_ex",
    	intTypeCol="int_type", intronExon, strandCol="strand", geneIdCol,
    	col=c(), names=c(), lasNames=1, outline=FALSE, plotLegend=TRUE,
    	cexLegend=1, xLegend="topright", yLegend=NULL, bgLegend="transparent",
    	legend=c(), addGrid=FALSE, ...)

### Arguments

`x` | Object of type `SummarizedExperiment`.
`sampleAnnoCol` | Which colummn of `colData` of `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.
`strandCol` | Column name (or number) that represents the strand of each row of assays in `x`. The values in the column are either "+", "-" or "*".
`geneIdCol` | Column name (or number) that represents the gene ID of each row of assays in `x`.
`col` | Vector containing box colours. It is either of size 1 or the same size as the number of boxes resulted based on the grouping of the samples defined by `sampleAnnoCol`.
`names` | Names to write under group of boxes.
`lasNames` | Orientation of the box names.
`outline` | If outline is TRUE the outlier points are drawn otherwise if FALSE (default) they are not.
`plotLegend` | Whether show legend (TRUE by default).
`cexLegend` | Size of the text in legend .
`xLegend, yLegend` | Position of legend in the plot. For more info see `x` and `y` parameters in `legend`.
`bgLegend` | Bakcground colour of the legend box. It is "transparent" by default.
`legend` | The replacement texts to be used in legend.
`addGrid` | Whether add a grid under the boxplots (FALSE by default).
`...` | Other arguments to pass to the `boxplot()` function.

### Value

Returns NULL

### Author(s)

Ali Oghabian

### See Also

`u12Boxplot`

### Examples

    u12BoxplotNb(mdsChr22Obj, sampleAnnoCol="type", lasNames=1,
        intExCol="int_ex", intTypeCol="intron_type", intronExon="intron",
        boxplotNames=c(), outline=FALSE, plotLegend=TRUE,
        geneIdCol="collapsed_transcripts_id", xLegend="topleft",
        col=c("pink", "lightblue", "lightyellow"), ylim=c(0,600000),
        ylab="FPKM", cex.axis=0.8)

[Package IntEREst version 1.2.2 Index]