u12DensityPlot: Density plot of fld changes of intron retention and exon-exon...

In gacatag/IntEREst: Intron-Exon Retention Estimator

Density plot of fld changes of intron retention and exon-exon junction levels

Description

Density plot of fold change of the retention levels of U12- vs U2- type intron, or exon-exon junction levels of the flanking exons. For the density plot of the foldchange of intron retention levels the u12DensityPlotIntron() function or u12DensityPlot() function with intronExon= "intron" can be used. For density plot of the foldchange of exon-exon junction levels use u12DensityPlot() function with intronExon= "exon".

Usage

u12DensityPlot(x, 
	type=c("U12", "U2Up", "U2Dn", "U2UpDn", "U2Rand"), 
	fcType="edgeR", sampleAnnotation=c(),  sampleAnnoCol=c(), 
	group=c(), intExCol="int_ex", intTypeCol="int_type", intronExon, 
	strandCol="strand", geneIdCol="collapsed_transcripts", 
	naUnstrand=FALSE, col=1, lty=1, lwd=1, plotLegend=TRUE, 
	cexLegend=1, xLegend="topright", yLegend=NULL, legend=c(), 
	randomSeed=NULL, xlab="", ...)

u12DensityPlotIntron(x, 
	type= c("U12", "U2Up", "U2Dn", "U2UpDn", "U2Rand"), 
	fcType= "edgeR", sampleAnnotation=c(),  sampleAnnoCol=c(), 
	group=c(), intExCol="int_ex", intTypeCol="int_type", 
	strandCol= "strand", geneIdCol= "collapsed_transcripts", 
	naUnstrand=FALSE, col=1, lty=1, lwd=1, plotLegend=TRUE, 
	cexLegend=1, xLegend="topright", yLegend=NULL, legend=c(), 
	randomSeed=NULL, xlab="", ...)

Arguments

x	Object of type SummarizedExperiment.
type	A vector that includes the type of introns to plot. Available options are U12 introns "U12", U2 introns at downstream of U12 introns "U2Dn", U2 introns at upstream of U12 introns "U2Up", U2 introns at upstream or downstream of U12 introns suitable for when the coorduinates in object x are unstranded (their strand is "*") "U2UpDn", random U2 introns from object x "U2Rand". Settings "U2Up", "U2Dn" and "U2UpDn" are useful only if the refernce is linearly ordered. References with exons only resulted by referencePrepare and unionRefTr are NOT necessarily linearly ordered.
fcType	Available as "fpkm" or "edgeR" (as default) corresponding to either log fold change of fpkm values or degeR normalized log fold change values.
sampleAnnoCol	Which colummn of colData of x to consider for plotting.
sampleAnnotation	A vector of size 2 which cotains values from colData of SummarizedExperiment object; e.g. if getAnnotation(x)[, sampleAnnoCol]= c("test", "test", "ctrl","ctrl", ...) , and the goal is to compare "test" and "ctrl" samples, sampleAnnotation should either be c("test", "ctrl") or c("ctrl", "test").
group	Vector to manually define the sample groups (or annotations). It is ignored if sampleAnnoCol is defined.
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.
naUnstrand	Replace unstranded results, i.e. introns or exon with "*" strand, with NA (to be excluded).
col	A vector with the size of 1 or the same size as the type parameter which includes the colour/colours of the plotted density lines (default=1).
lty	A vector with the size of 1 or the same size as the type parameter which includes the type of the plotted density lines (default=1).
lwd	A vector with the size of 1 or the same size as the type parameter which includes the width of the plotted density lines (default=1).
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.
legend	The replacement texts to be used in legend.
randomSeed	Seed value for random number generator.
xlab	The lable of the X axis of the plot; by default it is "".
...	Other parameter settings from the plot function.

Value

Returns NULL.

Author(s)

Ali Oghabian

See Also

exactTestInterest, lfc

Examples

u12DensityPlotIntron(mdsChr22Obj, 
    type= c("U12", "U2Up", "U2Dn", "U2UpDn", "U2Rand"), 
    fcType= "edgeR", sampleAnnoCol="test_ctrl", 
    sampleAnnotation=c("ctrl","test"), intExCol="int_ex", 
    intTypeCol="intron_type", strandCol= "strand", 
    geneIdCol= "collapsed_transcripts_id", naUnstrand=FALSE, col=c(2,3,4,5,6), 
    lty=c(1,2,3,4,5), lwd=1, plotLegend=TRUE, cexLegend=0.7, 
    xLegend="topright", yLegend=NULL, legend=c(), randomSeed=10,
    ylim=c(0,0.6), xlab=expression("log"[2]*" fold change FPKM"))

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