R/karyogram.R

In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

# karyogram <- function(nmr, chr_info) {
#     assert_has_columns(chr_info, c("chr", "length"))
#
#     n_chr <- nrow(chr_info)
#     plots <- list()
#
#     widest <- max(chr_info$length)
#
#     for (i in 1:n_chr) {
#         m <- query_methy(nmr, chr_info$chr[i], 1, chr_info$length[i])
#
#         bins <- round(seq(1, chr_info$length[i], length.out = 2^10))
#
#         bin_means <- binMeans(m$statistic > 0, x = m$pos, bx = bins)
#
#         df <- tibble(
#             pos = bins[-length(bins)],
#             methy_prop = as.numeric(bin_means),
#             count = attr(bin_means, "count")
#         )
#
#         plots[[i]] <- ggplot(df, aes(x = pos, y = 1, fill = methy_prop)) +
#             geom_tile() +
#             scico::scale_colour_scico(palette = 'imola', direction = -1) +
#             theme_void() +
#             theme(plot.margin = margin(0, 2, 0, 0)) +
#             ggtitle(chr_info$chr[i]) +
#             xlim(1, widest)
#     }
#
#     patchwork::wrap_plots(plots, ncol = 1, guides = "collect")
# }
#