u12BoxplotNb: boxplot U12 introns retention levels (or flanking exons...

In gacatag/IntEREst: Intron-Exon Retention Estimator

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)

gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.