Package index • wigglescout

All functions

bed_to_bw(): Parse a scored BED file and exports a bigWig file with given chromsizes

build_bins(): Build a unscored bins GRanges object.

build_bins_bw(): Build a tiles GRanges out of a bigWig file on a given bin size.

bw_bins(): Build a binned-scored GRanges object from a set of bigWig files

bw_global_coverage(): Calculate bigWig global coverage.

bw_heatmap(): Calculate heatmap matrix of a bigWig file over a GRanges or BED file

bw_loci(): Score a bigWig file list and a BED file or GRanges object.

bw_profile(): Calculate profile values of a bigWig file over a BED file.

.aggregate_scores(): Aggregate scores of a GRanges object on a field

.bw_ranges(): Score a GRanges object against a BigWig file

.calculate_bw_profile(): Calculate profile values of a bigWig file over GRanges object.

.calculate_matrix_norm(): Calculate a normalized heatmap matrix for a bigWig file over a BED file

.calculate_stretch_matrix(): Calculate matrix for stretch mode

.color_limits(): Calculate color limits from a value matrix and provided parameters

.colorscale(): Summary heatmap colorscale.

.convert_and_label_loci(): Internal processing of loci sets and labels.

.density_body(): Density 2d histogram plot

.fetch_bigwig(): Make a BigWigFile object out of a path or an URL

.filter_scatter_data(): Filter scatterplot data with quantile threshold on both axes

.filter_violin_data(): Filter violin plot data with quantile threshold

.get_wrapper_parameter_values(): Get matching parameters of a target function with current context

.granges_left_join(): GRanges left join operation

.heatmap_body(): Helper function for matrix heatmap plot

.heatmap_lines(): Helper function for calculating guide lines and labels in heatmap

.intersect_bw_and_granges(): Intersect a BigWig file over loci on a GRanges object

.is_multiple_loci(): Check if a variable contains a list of things or array of potentially file names

.key_value_string(): Make a string out of a named list.

.label_multiple_loci(): Label loci with a list of labels

.limited_size_caption_line(): Make a string out of a named list. Split into lines if too wide.

.loci_length(): Checks how many loci

.loci_to_granges(): Processes a loci and returns a GRanges object. Removes anything that is not a name field

.make_caption(): Make a string to put as caption in verbose mode. Includes system date.

.make_label_from_object(): Get a valid label

.make_norm_file_label(): Generate a human-readable normalization function string including

.make_norm_label(): Generate a human-readable normalization function string

.match_seqnames(): Match seqname lists and throws the relevant warning

.multi_bw_ranges(): Intersect a list of bigWig files with a GRanges object

.multi_bw_ranges_aggregated(): Intersect a list of bigWig files with a GRanges object and aggregate by name

.multi_bw_ranges_norm(): Intersect a list of bigWig files with a GRanges object (with background)

.multi_ranges_overlap(): Calculate overlap of one GRanges with a main GRanges object

.natural_sort_by_field(): Take a column of a data frame to use as row names, drop such column and reorder the data frame so row names follow natural order.

.preprocess_heatmap_matrix(): Preprocess heatmap values for plotting

.process_norm_mode(): Get a function out of a norm mode string.

.profile_body(): Helper function plots a profile from a dataframe

.profile_breaks(): Compute where the break ticks go in heatmap and profile

.profile_labels(): Make profile labels

.remove_top_by_mean(): Remove top loci in a GRanges column by mean of specified values

.round_ignore_null(): Round a value. If it's NULL, returns NULL.

.scatterplot_body(): Scatterplot of values in a GRanges object with mcols x and y

.summarize_matrix(): Summarize a intersect_bw_and_granges matrix

.summary_body(): Helper function for plotting a summary matrix

.theme_default(): Set default theme as classic with larger font size

.trunc_str(): Truncate a string to a max length

.validate_categories(): Validate a category array

.validate_filelist(): Validate an array of paths

.validate_group_col(): Validate that group col exists in granges

.validate_locus_parameter(): Validate that a locus parameter is valid. Checks for paths and also whether the parameter is otherwise a GRanges object, which is also valid.

.validate_profile_parameters(): Validate profile and heatmap relevant parameters

.validate_references(): Check that a list of bigWig files have the same Seqinfo. Throws a warning if they don't.

.validate_references_with_external_seqinfo(): Check that a list of bigWig files have the same Seqinfo as an external object (usually a pre-built tile set). Throws a warning if they don't.

.violin_body(): Internal function to plot ranges in violin plot with a highlighted GRanges.

get_datafile(): Return the full path of a test file in wigglescout package

get_heatmap_values(): Get heatmap fixture from bw_heatmap for test plotting

get_testfile(): Return the full path of a test file in wigglescout package

keep_canonical(): Filter out unplaced contigs and uncharacterized chromosomes from a GRanges object.

local_create_sample_bigwig(): Create a self-destructing local temporary bigwig based on a BED file and chromsizes array.

make_mock_bins(): Make a mock object that returns bins GRanges for test plotting

make_mock_bins_all(): Make a mock object that returns bins GRanges for test plotting

make_mock_profile(): Make a mock object from a fixture that has a profile result from bw_profile for test plotting

make_mock_summary(): Make a mock object from a fixture that has a summary result from bw_heatmap for test plotting

make_test_tiles(): Make example test tiles

plot_bw_bins_density(): Bin-based 2d histogram of a pair of bigWig files

plot_bw_bins_scatter(): Bin-based scatterplot of a pair of bigWig files

plot_bw_bins_violin(): Bin-based violin plot of a set of bigWig files

plot_bw_heatmap(): Plot a heatmap of a given bigWig file over a set of loci

plot_bw_loci_scatter(): Locus-based scatterplot of a pair of bigWig files

plot_bw_loci_summary_heatmap(): Summary heatmap of a categorized BED or GRanges object

plot_bw_profile(): Profile plot of a set of bigWig files

plot_gr_density(): Density plot of a precalculated GRanges object

plot_gr_scatter(): Scatterplot of a precalculated GRanges object

plot_gr_violin(): Violin plot of a precalculated GRanges object

tile_seqinfo(): Build a tiles GRanges out of a bigWig file on a given bin size.