spateo.io.bbs#
IO functions for calculating the bounding box.
Module Contents#
Functions#
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Compute the alpha shape (concave hull) of a set of points. |
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Return the convex hull of all nanoballs that have non-zero UMI (or at least > min_agg_umi UMI). |
- spateo.io.bbs.alpha_shape(x: numpy.ndarray, y: numpy.ndarray, alpha: float = 1, buffer: float = 1, vectorize: bool = True) Tuple[shapely.geometry.MultiPolygon | shapely.geometry.Polygon, List][source]#
Compute the alpha shape (concave hull) of a set of points. Code adapted from: https://gist.github.com/dwyerk/10561690
- Parameters:
- x
x-coordinates of the DNA nanoballs or buckets, etc.
- y
y-coordinates of the DNA nanoballs or buckets, etc.
- alpha
alpha value to influence the gooeyness of the border. Smaller numbers don’t fall inward as much as larger numbers. Too large, and you lose everything!
- buffer
the buffer used to smooth and clean up the shapley identified concave hull polygon.
- vectorize
Whether to vectorize the alpha-shape calculation instead of looping through.
- Returns:
The computed concave hull. edge_points: The coordinates of the edge of the resultant concave hull.
- Return type:
alpha_hull
- spateo.io.bbs.get_concave_hull(path: str, binsize: int = 20, min_agg_umi: int | None = None, alpha: float = 1.0, buffer: float | None = None) Tuple[shapely.geometry.Polygon, List][source]#
Return the convex hull of all nanoballs that have non-zero UMI (or at least > min_agg_umi UMI).
- Parameters:
- path
Path to read file.
- binsize
The number of spatial bins to aggregate RNAs captured by DNBs in those bins. By default it is 20, which is close to the size of a single cell. If stereo-seq chip used is bigger than 1 x 1 mm, you may need to increase the binsize.
- min_agg_umi
the minimal aggregated UMI number for the bucket.
- alpha
alpha value to influence the gooeyness of the border. Smaller numbers don’t fall inward as much as larger numbers. Too large, and you lose everything!
- buffer
the buffer used to smooth and clean up the shapley identified concave hull polygon.
- Returns:
The computed concave hull. edge_points: The coordinates of the edge of the resultant concave hull.
- Return type:
alpha_hull