lib5c.algorithms.filtering.bin_bin_filtering module¶
Module for smoothing bin-level 5C interaction matrices.
-
lib5c.algorithms.filtering.bin_bin_filtering.
bin_bin_filter
(array, filter_function, regional_pixelmap, threshold, filter_kwargs=None)[source]¶ Convenience function for filtering a bin-level matrix to a bin-level matrix.
- Parameters
array (np.ndarray) – The matrix to filter.
filter_function (Callable[[List[Dict[str, Any]]], float]) –
The filter function to use when filtering. This function should take in a “neighborhood” and return the filtered value given that neighborhood. A neighborhood is represented as a list of “nearby points” where each nearby point is represented as a dict of the following form:
{ 'value': float, 'x_dist': int, 'y_dist': int }
where ‘value’ is the value at the point and ‘x_dist’ and ‘y_dist’ are its distances from the center of the neighborhood along the x- and y-axis, respectively, in base pairs. See
lib5c.algorithms.filtering.filter_functions
for examples of filter functions and how they can be created.regional_pixelmap (List[Dict[str, Any]]) – The list of bins in this region.
threshold (int) – The threshold for defining the size of the neighborhood passed to the filter function, in base pairs.
filter_kwargs (Optional[Dict[str, Any]]) – Kwargs to be passed to the
filter_function
.
- Returns
The filtered matrix.
- Return type
np.ndarray
-
lib5c.algorithms.filtering.bin_bin_filtering.
bin_bin_filter_counts
(counts, function, pixelmap, threshold, function_kwargs=None)[source]¶ Non-parallel wrapper for
bin_bin_filter()
. Deprecated now thatbin_bin_filter()
is decorated with@parallelize_regions
.- Parameters
counts (Dict[str, np.ndarray]) – The counts dict to filter.
function (Callable[[List[Dict[str, Any]]], float]) – The filter function to use for filtering. See the description of the
filter_function
arg inbin_bin_filter()
.pixelmap (Dict[str, List[Dict[str, Any]]]) – The pixelmap describing the bins for
counts
.threshold (int) – The threshold for defining the size of the neighborhood passed to the filter function, in base pairs.
function_kwargs (Optional[Dict[str, Any]]) – Kwargs to be passed to the
function
.
- Returns
The dict of filtered counts.
- Return type
Dict[str, np.ndarray]
-
lib5c.algorithms.filtering.bin_bin_filtering.
find_nearby_bins
(index, regional_pixelmap, threshold)[source]¶ Finds the bins near a target bin as specified by an index.
- Parameters
index (int) – The index of the bin to look near.
regional_pixelmap (List[Dict[str, Any]]) – The list of bins in this region.
threshold (int) – The threshold for deciding if a bin is “nearby” or not, as a distance in base pairs.
- Returns
A list of nearby bins, where each nearby bin is represented as a dict of the following form:
{ 'index': int, 'distance': int }
where ‘index’ is the index of the bin within the region and ‘distance’ is the distance between this bin and the target bin.
- Return type
List[Dict[str, int]]