boxplot-method {IntEREst} | R Documentation

## boxplot - method

### Description

boxplot method for `SummarizedExperiment` objects.

### Usage

    ## S4 method for signature 'SummarizedExperiment'
    boxplot(x, sampleAnnoCol=NA,
    	intexTypeCol="int_type", intexType=c(), col="white", boxplotNames=c(),
    	lasNames=3, outline=FALSE, addGrid=FALSE, ...)

### Arguments

`x` | Object of type `SummarizedExperiment` generated by either `interest()`, `interest.sequential()` or `readInterestResults()`.
`sampleAnnoCol` | Which colummn of `colData` in `x` to consider for plotting.
`intexTypeCol` | Column name (or number) that represents what type of intron/exon each row of `x` assays represents.
`intexType` | A vector of characters describing types of introns/exons to be plotted. They must be elements in the `intexTypeCol` column of the rowData of `x`. rowData of `x` is a dataframe that includes various annotations of the introns/exons.
`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 the row (intron/exon) annotation names 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()` and `axis` function.

### Value

Returns NULL.

### Author(s)

Ali Oghabian

### See Also

Class: `SummarizedExperiment-class` Method: `counts-method` `plot-method`

### Examples

    #Plotting U12- vs U2-type introns
    par(mar=c(8,4,2,1))
    boxplot(x=mdsChr22Obj, sampleAnnoCol="type", intexTypeCol="intron_type",
    	intexType=c("U2", "U12"),
    	col=rep(c("yellow", "orange"),3),
    	boxplotNames=c(), lasNames=3, outline=FALSE,
    	addGrid=TRUE)

[Package IntEREst version 1.4.1 Index]