multifreqpoly: Multiple frequency polygon plot
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) References Examples

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.

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,...)

`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"

Frequency polygon plots.

Zongli Xu

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

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()
}