multifreqpoly: Multiple frequency polygon plot

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Multiple frequency polygon plot

Description

Produce Frequency polygon plot for each column of a numeric data matrix. Similar to multidensity function, the plot can be used to inspect data distribution but with much faster speed.

Usage

multifreqpoly(mat, nbreaks=100, col=1:ncol(mat), xlab="", 
              ylab="Frequency",legend = list(x = "top", fill=col,
              legend = if(is.null(colnames(mat))) paste(1:ncol(mat)) 
              else colnames(mat)),append=FALSE,...)

Arguments

mat	A numeric matrix
nbreaks	The number of bins for frequency counting
col	Line plot color code, the length should be equal to the number of columns in mat
xlab	x-axis lable
ylab	y-axis lable
legend	A list of arguments that get passed to the function "legend"
append	TRUE or FALSE, whether to create a new figure or append to the current figure.
...	Further arguments that get passed to the function "plot"

Value

Frequency polygon plots.

Author(s)

Zongli Xu

References

Zongli Xu, Liang Niu, Leping Li and Jack A. Taylor, ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research 2015.

Examples

x=matrix(rnorm(10000),nrow=2000,ncol=5)
multifreqpoly(x,nbreaks=15,legend=list(x="topright",fill=1:ncol(x),legend=paste("V",1:5,sep="")))

if (require(minfiData)) {
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
mraw <- getmeth(rgSet)
beta<-getB(mraw)
jpeg("dist_raw.jpg")
multifreqpoly(beta,col=1:ncol(beta))
dev.off()
}

xuz1/ENmix documentation built on Nov. 24, 2024, 4:31 a.m.