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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/u12BoxplotNb.R

Description

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

Usage

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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

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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)

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.