feat: adding new CN characterizing functions.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dlptools
 Title: DLPTools: Handling DLP+ Data
-Version: 0.3.17
+Version: 0.3.18
 Authors@R: 
     person("Ben", "Furman", , "bfurman@bccrc.ca", role = c("aut", "cre"))
 Description: A collections of functions for basic manipulation and plotting of

NAMESPACE

@@ -4,12 +4,15 @@ export("%>%")
 export(ASCN_COLORS)
 export(ASCN_PHASE_COLORS)
 export(BAF_COLORS)
+export(BASE_PLOT_THEME)
 export(CNV_COLOURS)
 export(DEFAULT_CONTINUOUS_COLOR_RANGE)
+export(GEN_PLOT_COLS)
 export(RAW_COPY_COLORS)
 export(STATE_COLORS)
 export(add_centromere_locations)
 export(add_missing_bins_for_cells)
+export(add_telomere_positions)
 export(add_tip_ancestors_to_df)
 export(basic_tile_plot)
 export(cell_cn_profile)
@@ -22,7 +25,10 @@ export(compute_tip_sibling_distances)
 export(convert_dists_to_pairwise)
 export(convert_long_reads_to_wide)
 export(create_expected_bins)
+export(cust_mode)
 export(expand_length_to_bins)
+export(extract_ploidy_cn_feature)
+export(extract_segment_position_feature)
 export(extract_sigminer_wang_features)
 export(extract_wu_features)
 export(factor_column_mixedsort)
@@ -41,6 +47,7 @@ export(get_tips_that_avoid_redundant_comps)
 export(import_annotations_df)
 export(import_clones)
 export(import_dlp_files)
+export(import_telos_file)
 export(import_tree)
 export(library_from_cell)
 export(load_chrom_info_file)
@@ -51,8 +58,11 @@ export(make_corrupt_tree_heatmap)
 export(make_tree_plot_obj)
 export(map_states_to_letters)
 export(mark_bins_overlapping_centromeres)
+export(mark_cn_relative_to_ploidy)
 export(mark_mask_regions)
+export(mark_segs_chromosome_span)
 export(medicc_profiles_to_foreground)
+export(mode_ploidy)
 export(pairwise_bin_difference)
 export(plot_bg_state_highlight)
 export(plot_fg_state_highlight)

R/bin_filling.R

@@ -1,31 +1,3 @@
-#' loading UCSC chromosome length files
-#' @param version default "hg19", can also load "hg38"
-#' @return tibgble of chromosome, total length, etc.
-#' @export
-load_chrom_info_file <- function(version = c("hg19", "hg38")) {
-  version <- match.arg(version)
-
-  chrom_files <- list(
-    hg19 = "hg19_chromInfo.txt.gz",
-    hg38 = "hg19_chromInfo.txt.gz"
-  )
-
-  chrom_info <- get_package_file_path(chrom_files[version]) |>
-    vroom::vroom(
-      col_names = c("chr", "total_length", "misc"),
-      show_col_types = FALSE
-    ) |>
-    dplyr::filter(
-      # remove the unnecessary chromosomes
-      stringr::str_detect(chr, "_|M", negate = TRUE)
-    ) |>
-    dplyr::mutate(
-      chr = stringr::str_replace(chr, "chr", "")
-    )
-
-  return(chrom_info)
-}
-
 #' For a given length, create bins of a given size
 #'
 #' e.g., length = 10, bin = 5, will get bins: 1-5, 6-10
@@ -128,7 +100,7 @@ add_missing_bins_for_cells <- function(
 #' other states to fill in.
 #'
 #' @param state_df dataframe of state data with NAs for some bins that need
-#' to be filled in. E.g., after dlptools::running add_missing_bins_for_cells()
+#' to be filled in. E.g., after dlptools::add_missing_bins_for_cells()
 #' @export
 #' @importFrom rlang .data
 fill_state_from_neighbours <- function(state_df, cols_to_fill = c("state")) {