S1G-J.md

S1G-J

2025-09-11

# Libraries
library(karyoploteR)
library(rtracklayer)
library(dplyr)
library(ragg)  # headless PNG device

# knitr defaults: write images to a tracked folder for GitHub
knitr::opts_chunk$set(
  fig.path  = "figures/S1G-J-",
  dev       = "ragg_png",
  dpi       = 150,
  out.width = "100%",
  message   = FALSE,
  warning   = FALSE
)

# -------- Parameters --------
bed_path <- "/groups/gerlich/labinfo/Projects/FedericoTeloni/Results/Datasummeries/jupyter/HS17/HS17.bed"
chroms   <- paste0("chr", c(1:22, "X"))   # no chrY
genome   <- "hg19"

# -------- Load once --------
bed_df <- read.table(bed_path, header = FALSE, sep = "\t", stringsAsFactors = FALSE)
colnames(bed_df) <- c("chr", "start", "mismatch", "cut_state")

# -------- Helpers --------
init_karyoplot <- function(genome, chroms) {
  kp <- plotKaryotype(genome = genome, chromosomes = chroms, plot.type = 6)
  kpDataBackground(kp, color = "white")
  kp
}

plot_segments <- function(kp, df, col = "red", lwd = 2, lty = 1) {
  if (nrow(df) == 0) return(invisible(NULL))
  kpSegments(kp,
             chr = df$chr,
             x0  = df$start, x1 = df$start,
             y0  = 0,        y1 = 1,
             col = col, lwd = lwd, lty = lty)
}

# Subsets
mismatch_0 <- bed_df %>% filter(mismatch == 0)
mismatch_1 <- bed_df %>% filter(mismatch == 1)

# Plot
kp <- init_karyoplot(genome, chroms)
plot_segments(kp, mismatch_0, col = "red", lwd = 2, lty = 1)  # solid
plot_segments(kp, mismatch_1, col = "red", lwd = 2, lty = 3)  # dotted

yes_data <- bed_df %>% filter(cut_state == "YES")

kp <- init_karyoplot(genome, chroms)
plot_segments(kp, yes_data, col = "red", lwd = 2, lty = 1)