Package index • GaitiLabUtils

All functions

LMM_test(): Perform a nested t-test using LMMs.

auto_crop(): Autocrop plot

build_adjacency_table(): Build adjacency table

compute_neighbor_metrics(): Compute neighbor metrics

compute_perm_pval(): Compute p-val permutation testing

compute_shuffled_autocorr(): spatialCrossCorTest

create_dir(): Create directory

create_hm(): Plot heatmap + save

create_lookup_table(): Create annotation lookup table

create_polygon(): create polygons

default_theme(): Standard theme for figures

find_neighbouring_spots(): Find neighbouring spots

find_neighbours_in_window(): Find neighbours in window

find_neighbours_in_window_around_spot(): Find neighbours in window around spot

generate_pairs(): Generate pairs,

geom_signif_lmm(): geom signif with lmm test. See geom_signif from ggsignif for more information

get_cell_dims(): Get size of heatmap (in mm)

get_cell_function(): Setup cell function for ComplexHeatmap

get_current_date(): Obtain current date

get_density(): Get density of points in 2 dimensions.

get_name(): Extract name from filepath

get_optimal_output_size(): Determine optimal ComplexHeatmap size

get_pcs(): Function for getting get_pcs

init_logging(): Set up logging

inspect_k_nearest_neighbors(): Inspect k nearest Neighbors

inspect_neighbors(): Inspect Neighbors

jaccard_similarity(): Compute Jaccard similarity

log_debug(): Logging functions: log_debug

log_error(): Logging functions: log_error

log_fatal(): Logging functions: log_fatal

log_info(): Logging functions: log_info

log_warn(): Logging functions: log.warn

merge_dfs(): Merge list of dataframes

one_sample_perm_test_pval(): Compute p-val for one-sample permutation test

save_hm(): Save heatmap

set_wd(): Set working directory automatically

setup_default_argparser(): initialize argparser

transpose_df(): Transpose dataframe

visualize_transcripts(): Visualize transcripts