R/ASCATScatterView.R

In szilvajuhos/sarek.pathfindr: Scoring somatic and germline variants for cancer genome analysis

ASCATScatterView <- function(ascat_binned) {
  if (exists('ascat_binned')) for (sample in unique(ascat_binned$sample)) {
    cat('ASCAT: ',sample)
    g=ggplot()+
      ggplot2::expand_limits(y=c(.5,1))+
      ggplot2::expand_limits(x=c(.3,3))+
      ggplot2::geom_point(ggplot2::aes(x = tratio,y = tmaf,col=chr),data=ascat_binned[sample][tratio<3])+
      ggplot2::xlab('Tumor (1Mb mean) DNA ratio')+
      ggplot2::ylab('Tumor (1Mb mean) major allele ratio')+
      ggplot2::scale_y_continuous(breaks = seq(0.5,1,0.1)) +
      ggplot2::scale_x_continuous(breaks = seq(0.5,2.5,0.1))+
      ggplot2::theme(panel.grid.minor.x = ggplot2::element_blank(),
            panel.grid.major.x = ggplot2::element_line(colour="grey", size=0.2),
            panel.grid.major.y = ggplot2::element_line(colour="grey", size=0.2),
            panel.grid.minor.y = ggplot2::element_blank()
      )
  }
  g
}