R/tss_tts.variants.plot.R

In greymonroe/polymorphology: Functions from Monroe et al 2022

#' plot relative position of polymorphisms in relation to gene bodies
#' @param positions object creatd by tss_tts.variants() with columns pos and loc
#' @param window window size for counting variants, default is 10
#' @return a ggplot object plotting the tss and tts data
#' @import data.table
#' @import ggplot2
#' @export
tss_tts.variants.plot<-function(positions, window=10, color="green4"){

  positions$bins<-as.numeric(as.character(cut(positions$pos, breaks=seq(-3000, 3000, by=window), labels=seq(-3000, 3000, by=window)[-1])))
  positions_means<-positions[!is.na(bins),.N, by=.(bins, loc)]
  plot<-ggplot(positions_means, aes(x=bins, y=N))+
    geom_line(aes(group=1), col=color, size=0.25)+
    facet_grid(~loc, scales = "free")+
    theme_classic(base_size = 6)+
    scale_x_continuous(name="Relative genomic positions")+
    geom_vline(xintercept=0, linetype="dashed", size=0.25)+
    scale_y_continuous(name="Variants")+
    theme(panel.background = element_rect(colour = "black", size=0.5),
  axis.line.y = element_blank())
  return(plot)

}