R/plotROCfromFiles.R

In jvanheld/stats4bioinfo: Utilities for the book "Statistics for bioinformatics"

## ##############################################################
## Plot a series of ROC curves from a set of data files.
## Each input file must be a tab-delimted text file with 3 columns:
## - score
## - frequency of true positive above the score (e.g.regulons)
## - frequencies of false positive above the score (e.g. random gene selections)
##
## One separate curve is plotted for each data file. This is
## convenient to compare performances of a program with different
## parameters, or to compare the performances obtained with different
## programs
plotROCfromFiles <- function(data.files, ## A list of files
                                       line.type = "l", ## line type for the plots
                                       main='ROC curve -  regulons versus random gene selections',
                                       xlab='random gene selections',
                                       ylab='regulons',
                                       ... ## Other parameters are passed to the plot() function
) {
  
  ## Plot the background lines
  plotROCframe(main=main,xlab=xlab,ylab=ylab,...)
  #   plot(c(0,1),
  #        c(0,1),
  #        type='l',
  #        panel.first=grid(col='#000000'),
  #        main=main,
  #        xlab=xlab,
  #        ylab=ylab,
  #        ...
  #        )
  #   lines(c(1,0),c(0,1),type='b',col='#BBBBBB')
  
  i <- 0
  data.colors <- vector()
  
  for (file.data in data.files) {
    ## Assign a color to each data file
    i <- i+1
    data.colors[file.data] <- i
    
    ## Read the data file
    setwd(dir.compa); x <- read.table(file.data,header=T)
    names(x) <- c('sig', 'regulons', 'random.genes')
    
    if (sum(x$random.genes) < sum(x$regulons)) {
      lines(x$random.genes, x$regulons,
            type=line.type,
            col=data.colors[file.data],
            lwd=2
      )
    } else {
      lines(1- x$random.genes, 1- x$regulons,
            type=line.type,
            col=data.colors[file.data],
            lwd=2
      )
    }
  }
  legend(0.5,0.5,legend=data.files,col=data.colors,lwd=2,bty="n")
  
}