Package index • dlptools

All functions

ASCN_COLORS: colors for signals results of allele balances

ASCN_PHASE_COLORS: ASCN phase colors

CNV_COLOURS: standard colors used in dlp plots

DEFAULT_CONTINUOUS_COLOR_RANGE: min, median, max for a continuous color range

STATE_COLORS: alias of standard colors used in dlp plots

add_centromere_locations(): add centromere information to reads by chromosome

add_missing_bins_for_cells(): Add back chr, start, end of bins missing from cells

add_tip_ancestors_to_df(): add parent node labels to a dataframe of cell ids with states

basic_tile_plot(): create a tile plot of read state calls.

bme_vec(): picks beginning, middle, and end of a vector to handle when vectors that are too long are passed

build_left_annot(): builds the left-side annotations of the cells

cell_id_order_as_plotted(): grab cell ids in the order that they are plotted

cell_states_to_strings(): collapse cell states to strings

characterize_foreground_allele_state_changes(): mark types of allele specific foreground state changes

characterize_foreground_total_state_changes(): mark the types of change between a parent node state and the tip.

check_args(): confirms arguments are compatible for the plotting wrapper

check_if_state_columns_are_valid(): internal check for using the characterization function

check_or_fetch_clone_palette(): confirm pallete given has enough colors or generate one

check_the_vibe(): just a silly alias.

chr_name_check(): internal for checking the names of chromosome columns in a dataframe.

compute_tip_sibling_distances(): measure string distances between sibling tips

convert_long_reads_to_wide(): convert long format reads to wide format

create_chromosome_column_fct(): create a sorted factor vector of chromosomes

create_expected_bins(): create bins of given size for a genome

does_palette_cover_plot_vals(): internal to confirm color choice was ok

expand_length_to_bins(): For a given length, create bins of a given size

factor_column_mixedsort(): naturally sort a column from a dataframe.

fetch_continuous_color_ramp(): internal function for setting up heatmap continuous range colors chooses defaults, unless overwritten by user.

fetch_heatmap_color_palette(): grab colors for various hm possibilities.

fill_state_from_neighbours(): infer missing data using the upstream neighbour bin

format_sitka_tree(): clean tree tip labels and drop any locus tips from sitka trees

format_states_for_hm(): format states for plotting in a heatmap

generate_hm_image(): generate a ComplexHeatmap::Heatmap image, either to console or file.

generate_state_hm(): creates a complex heatmap of a given matrix of states.

get_clone_id_label_positions(): get a row number of where to place each clone label.

get_clone_members(): create list of list of cell_ids that belong to each clone id.

get_column_metrics(): get plotted values bounds

get_dist_to_sibs(): get distance of states to siblings for a tree tip

get_package_file_path(): retrieve file path to package data files

get_tip_parents(): resolve who the immediate parent nodes are for each tip.

get_tips_that_avoid_redundant_comps(): get tips labels that will avoid duplicate sibling comparisons

import_annotations_df(): read an annotations file (t(c)sv)

import_clones(): read a clones t(c)sv file

import_dlp_files(): generic function to import dlp files

import_tree(): read a tree from a file in newick format

is_not_numeric_lacks_order(): confirms a vector is not numeric and is unorderd

library_from_cell(): extract library ID from the typically formatted cell_ids

load_chrom_info_file(): loading UCSC chromosome length files

load_mask_file(): internal to control mask file loading.

load_ucsg_cenrtomeres(): load and prep default centromerefiles from UCSC

make_clone_palette(): generate a color palette for clone labels

make_corrupt_tree_heatmap(): create a complex heatmap object with a tree.

make_tree_plot_obj(): create a ggplot object of a phylogenetic tree

map_states_to_letters(): convert a vector of states to letters

mark_bins_overlapping_centromeres(): add boolean if bin overlaps with a centromere.

mark_mask_regions(): add a mask column to a dataframe

medicc_profiles_to_foreground(): medicc profiles files to foreground assessment

plot_bg_state_highlight(): generate a plot of just the background states, making the foreground white.

plot_fg_state_highlight(): generate a plot of just the foreground states, making the background white.

plot_heatmap_of_tip_changes(): make a plot of just the foreground events

plot_state_hm(): main hm building function

pull_chr_from_col_name(): extract chromosome name from a bin name (chr_start_end)

pull_info_from_cell_id(): generic extractor of info contained in cell ids

read_medicc_profiles(): ingest a medicc profiles file

read_medicc_tree(): read medicc tree to phylo object.

reads_to_segs(): convert reads table to segments table

rle_states(): convert states to run length encoding

sample_from_cell(): extract sample ID from the typically formatted cell_ids

segs_to_reads(): split segments into bins of a requested size.

sort_df_by_cell_order(): sort a table given a vector of cell_ids