comparison probecoverage.r @ 1:ebe5ec2e244d draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 0d963d33685a407873cd17924c7ec2b6255b006f

0:dbeb4a0abfc6

}

## function

cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome)

## end of function
## let's do a dataframe before plotting
maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20
graphpoints <- data.frame(1:maxdepth)

graphpoints <- melt(graphpoints, id.vars="Depth", variable.name="Samples", value.name="sample_value")

## GRAPHS

pdf(file=args$output)
ggplot(data=graphpoints, aes(x=Depth, y=sample_value, group=Samples, colour=Samples)) +
      geom_line(size=1) +
      scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) +
      scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10)) +
      labs(x=args$xlab, y=args$ylab, title=args$title) +
      theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7))

devname=dev.off()

1:ebe5ec2e244d

}

## function

cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome)
scaleFUN <- function(x) sprintf("%.3f", x)

## end of function
## let's do a dataframe before plotting
maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20
graphpoints <- data.frame(1:maxdepth)

graphpoints <- melt(graphpoints, id.vars="Depth", variable.name="Samples", value.name="sample_value")

## GRAPHS

pdf(file=args$output)
ggplot(data=graphpoints, aes(x=Depth, y=sample_value, colour=Samples)) +
      geom_line(size=1) +
      scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) +
      scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10), labels=scaleFUN) +
      labs(x=args$xlab, y=args$ylab, title=args$title) +
      theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7))
      
      
##      facet_wrap(~Samples, ncol=2)

devname=dev.off()