function to plot outline over a region in visium data

visium_region_outline.py

# install alpha_shapes from https://github.com/panosz/alpha_shapes
# adata.obsm['region_inside'] contains a (n_visium_spots, k_regions) binary array,
# where 1 indicates visium spot beplonging to a given regions
# adata.obsm['spatial'] contains position of each of n_visium_spots

from alpha_shapes import Alpha_Shaper, plot_alpha_shape
from tqdm import tqdm

def plot_visium_region_outline(adata):
    alpha_scaling=1
    outline_list = []
    for i in tqdm(range(adata.obsm['region_inside'].shape[1]-1)):
        try:
            nodule_points = adata.obsm['spatial'][adata.obsm['region_inside'][:,i] == 1]
            if len(nodule_points) != 0:

                #double
                new_coord_hex = []
                for j in range(nodule_points.shape[0]):
                    new_coord_hex.append(np.array(hexagon_points(nodule_points[j], 198/2+16)))
                new_coord_hex = filter_near_duplicates(np.array([x for s in new_coord_hex for x in s]))
                shaper = Alpha_Shaper(new_coord_hex)
                try:
                    alpha = 12
                    alpha_shape = shaper.get_shape(alpha=alpha)
                    try:
                        outline_list.append(alpha_shape.boundary.coords.xy)
                    except NotImplementedError:
                        alpha = 5
                        alpha_shape = shaper.get_shape(alpha=alpha)
                        outline_list.append(alpha_shape.boundary.coords.xy)
                except AttributeError:
                    alpha = 2
                    alpha_shape = shaper.get_shape(alpha=alpha)
                    outline_list.append(alpha_shape.boundary.coords.xy)

                # outline_list.append(outwords_points[hull].T)
                # plt.plot(*outwords_points[hull].T, c='k')
                # plt.scatter(*nodule_points.T, c='grey')
            else:
                print('empty ' + str(i))
        except IndexError:
            print(i)
      if ax is None:
        fig, ax = plt.subplots(figsize=(8,8))

    for i in range(len(outline_list)):
        ax.fill(*outline_list[i], fill=False, edgecolor='black', lw=1, zorder=3)    
    ax.set_aspect('equal')
    ax.spines[['right', 'top', 'left', 'bottom']].set_visible(False)
    ax.set_xticks([])
    ax.set_yticks([])
    ax.set_xticklabels([])
    ax.set_yticklabels([])