R/mutect2View.R

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

mutect2View <- function(mutect2_table) {
  g_mutect2 <- NULL
  alltier1 <- get("alltier1",pfenv)
  alltier2 <- get("alltier2",pfenv)
  
  cat(PFconfig$mutect2_file, sep = '\n')
  if (exists('mutect2_table'))
    for (sample in sort(unique(mutect2_table$sample))) {
      par(mai = c(1, 4, 0, 2))
      
      # Basic plot element
      g_basic =
        ggplot() +
        ylab('Somatic mutation allele ratio') +
        expand_limits(y = c(0, 1)) +
        expand_limits(x = c(0, 3210e6)) +
        scale_fill_manual(
          values = c(
            "A>C" = "#1B9E77",
            "A>G" = "#D95F02",
            "A>T" = "#7570B3",
            "C>A" = "#E7298A",
            "C>G" = "#66A61E",
            "C>T" = "#E6AB02",
            "del" = "#A6761D",
            "ins" = "#666666"
          )
        ) +
        scale_shape_manual(
          values = c(
            "A>C" = 21,
            "A>G" = 21,
            "A>T" = 21,
            "C>A" = 21,
            "C>G" = 21,
            "C>T" = 21,
            "del" = 24,
            "ins" = 25
          )
        ) +
        scale_color_manual(values = c('<5' = 'lightgrey', '≥5' = 'black')) +
        theme(
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          axis.title.x = element_blank(),
          axis.text.x = element_blank(),
          axis.ticks.x = element_blank()
        ) +
        geom_segment(
          mapping = aes(
            x = starts,
            xend = starts,
            y = 0,
            yend = 1
          ),
          data = chrsz,
          inherit.aes = F,
          alpha = 1 / 5
        ) +
        geom_text(
          aes(
            x = starts + 0.5 * length,
            y = 0,
            label = label
          ),
          data = chrsz,
          inherit.aes = F
        )
      
      
      # Mutect2 plot
      cat('Mutect2: ', sample)
      temp = unique(mutect2_table[on=sample][, .(cumstart,
                                              reads,
                                              AFreq,
                                              type,
                                              SYMBOL,
                                              Protein_position,
                                              Amino_acids,
                                              IMPACT)])
      g_mutect2 = g_basic +
        xlab(paste('Mutect2: ', sample)) +
        geom_point(
          data = temp,
          mapping = aes(
            x = cumstart,
            y = AFreq,
            fill = type,
            shape = type,
            col = reads
          ),
          alpha = 1
        ) +
        geom_label_repel(
          data = temp[SYMBOL %in% alltier1 &
                        IMPACT %in% c('MODERATE', 'HIGH'), ],
          mapping = aes(
            x = cumstart,
            y = AFreq,
            label = paste(SYMBOL, Protein_position, Amino_acids)
          ),
          inherit.aes = F,
          size = 3,
          nudge_y = 0.2,
          col = 'black'
        ) +
        geom_label_repel(
          data = temp[SYMBOL %in% alltier2 &
                        IMPACT %in% c('MODERATE', 'HIGH'), ],
          mapping = aes(
            x = cumstart,
            y = AFreq,
            label = paste(SYMBOL, Protein_position, Amino_acids)
          ),
          inherit.aes = F,
          size = 3,
          nudge_y = 0.2,
          col = 'grey'
        )
    }
  g_mutect2
}