R/PoisTestPlot.R

In takahirosuzuki1980/InfiniumDiffMetMotR: Motif Overrepresentation analysis for Illumina Methylation Arrays

#' Plot a p-value plot
#' 
#' Vidualization of the Poisson test p-value.
#' The value is -10logP
#' red dots represent p <= 0.00001
#' 
#' @param motif_counts_matrix motif counts matrix output from countMatrix
#' @param motif_name PWM ID
#' @param seq_range range to be analyzed
#' 
#' @importFrom graphics plot
#' @importFrom graphics par
#' 
#' @keywords Poisson test, p-value, plot
#' @export

PoisTestPlot <- function(motif_counts_matrix,  motif_name = "motif", seq_range){
   Pvals <- motif_counts_matrix[,4]
   pois2 <- -log10(Pvals)
   pois2 <- replace(pois2, which(pois2 == Inf), 500)    #In the case of adjusted P-value=0, relace infinity to 500
   poisPylim <- c(0, max(pois2)*1.1)    #y max of the plot area
   poisPxlim <- seq_range    #range to be plotted
   ylab <- "Log10P"    #y-axis label
   main <- paste(motif_name, "(Pois Pvalue)", sep="")
   plot(rownames(motif_counts_matrix), pois2, ylim=poisPylim, xlim=poisPxlim, ylab=ylab, xlab="Distance from CpG", main=main, type="l", pch=20, cex.axis=0.7)
   par(new=T)
   ## if the adjested p-value is significant (p <= 0.00001), the plots turn to red
   sigPois2 <- pois2[which(pois2 > 5)]
   plot(as.numeric(names(sigPois2)), sigPois2, ylim=poisPylim, xlim=poisPxlim, ylab="", xlab="", main=main, col="red", pch=21,cex.axis=0.7)
}