plot-method: plot - method

plot-methodR Documentation

plot - method

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")

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