boxplot-method: boxplot - method
In IntEREst: Intron-Exon Retention Estimator

Description Usage Arguments Value Author(s) See Also Examples

boxplot method for SummarizedExperiment objects.

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

`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.

Returns NULL.

Ali Oghabian

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

#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)