plot-method: plot - method

In IntEREst: Intron-Exon Retention Estimator

Description

plot method for SummarizedExperiment objects.

Usage

## S4 method for signature 'SummarizedExperiment,ANY'
plot(x, summary="none", 
	subsetRows=NULL, what="scaled", intronExon="intron", 
	logScaleBase=NULL, logPseudoCnt=1, plotLoess=TRUE, 
	loessCol="red", loessLwd=1, loessLty=1, cexText=1, 
	marPlot=c(2,2,2,2), mgpPlot=c(1, 1, 0), cexAxis=1, 
	writeCor=TRUE, corCex=1, corMethod="pearson", corCol="grey63", 
	upperCorXY=c("topleft", NULL), lowerCorXY=c("topleft", NULL), 
	na.rm=TRUE,	cex=1, sampleAnnoCol=c(), lowerPlot=FALSE, 
	upperPlot=TRUE, ...)

Arguments

x	Object of type SummarizedExperiment generated by either interest(), interest.sequential() or readInterestResults().
summary	Whether to plot the mean or median of the values over the sample with the same annotations, or plot the values for each individual sample separately. The available options are "mean", "median", or "none".
subsetRows	Vector either constructed of TRUE/FALSE values or constructed of numeric values that could be used to choose rows of x i.e. the SummarizedExperiment object.
what	Whether plot "scaled" (default) or read counts ("counts").
intronExon	Whether plot intron retention, i.e. "intron" (default) or exon-junction "exon".
logScaleBase	Base of the log transform of the values, if defined. By default the value is NULL meaning that the values would not be log transformed.
logPseudoCnt	Pseudocount for the log transformation (default=1).
plotLoess	Whether fit and plot LOESS curve line (default="red").
loessCol	loess line colour (default="red").
loessLwd	loess line width (default=1).
loessLty	loess line type (default=1).
cexText	Size of the text for sample names or annotations (default=1).
marPlot	Plot margins (default=c(2,2,2,2)). See ?par for more information.
mgpPlot	Plotting mgp parameter (default=c(1, 1, 0)). See ?par for more information.
cexAxis	Size of the text for the axis (default=1).
writeCor	Write correlation values (default=TRUE).
corCex	Text size of correlation values (default=1).
corMethod	Method used for correlation calculation. For more information see cor from stats package of R.
corCol	Color of the text of correlation (default="grey").
upperCorXY	The coordinates of the correlation text in the upper panel plots ( default= c("topleft", NULL) ).
lowerCorXY	The coordinates of the correlation text in the lower panel plots ( default= c("topleft", NULL) ).
na.rm	whether remove the rows with missing values (default=TRUE).
cex	size of the plot text and symbols (default=1).
sampleAnnoCol	Which colummn of colData of object SummarizedExperiment to consider for plotting.
lowerPlot	Whether plot the lower panel (default=FALSE).
upperPlot	Whether plot the upper panel (default=TRUE).
...	Other arguments to pass to the plot() function.

Value

Returns NULL.

Author(s)

Ali Oghabian

See Also

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

Examples

geneId<- paste("gene", c(rep(1,5), rep(2,5), rep(3,5), rep(4,5)), 
	sep="_")
readCnt1<- sample(1:100, 20)
readCnt2<- sample(1:100, 20)
readCnt3<- sample(1:100, 20)
readCnt4<- sample(1:100, 20)
fpkm1<- readCnt1/(tapply(readCnt1, geneId, sum))[geneId]
fpkm2<- readCnt2/(tapply(readCnt2, geneId, sum))[geneId]
fpkm3<- readCnt3/(tapply(readCnt3, geneId, sum))[geneId]
fpkm4<- readCnt4/(tapply(readCnt4, geneId, sum))[geneId]

# Creating object using test data
interestDat<- data.frame( 
		int_ex=rep(c(rep(c("exon","intron"),2),"exon"),4),
		int_ex_num= rep(c(1,1,2,2,3),4),         
		gene_id= geneId,
		sam1_readCnt=readCnt1,
		sam2_readCnt=readCnt2,
		sam3_readCnt=readCnt3,
		sam4_readCnt=readCnt4,
		sam1_fpkm=fpkm1,
		sam2_fpkm=fpkm2,
		sam3_fpkm=fpkm3,
		sam4_fpkm=fpkm4
)
readFreqColIndex<- grep("_readCnt$",colnames(interestDat))
scaledRetentionColIndex<- grep("_fpkm$",colnames(interestDat))

scalRetTmp<- as.matrix(interestDat[ ,scaledRetentionColIndex])
colnames(scalRetTmp)<-gsub("_fpkm$","", colnames(scalRetTmp))

frqTmp<- as.matrix(interestDat[ ,readFreqColIndex])
colnames(frqTmp)<-gsub("_readCnt$","", colnames(frqTmp))


InterestResultObj<- InterestResult(
	resultFiles=paste("file",1:4, sep="_"),
	rowData= interestDat[ , -c(readFreqColIndex, 
		scaledRetentionColIndex)],
	counts= frqTmp,
	scaledRetention= scalRetTmp,
	scaleLength=TRUE, 
	scaleFragment=FALSE,
	sampleAnnotation=data.frame(
		sampleName=paste("sam",1:4, sep=""),
		gender=c("M","M","F","F"), row.names=paste("sam", 1:4, sep="")
	)
)

InterestResultObj2<- addAnnotation(x=InterestResultObj,
	sampleAnnotationType="health",
	sampleAnnotation=c("healthy","unhealthy","healthy","unhealthy")
)

#Plotting
plot(InterestResultObj)
plot(InterestResultObj, sampleAnnoCol="gender", summary="mean")
plot(InterestResultObj2, sampleAnnoCol=3, summary="mean")
plot(InterestResultObj2, summary="none")

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