作成日:2024年4月9日
マルコフ連鎖の実装
def prepare_markov_simulation(self, verbose=False):
"""
Pick up cells for Markov simulation.
Args:
verbose (bool): If True, it plots selected cells.
"""
# Sample uniformly the points to avoid density driven effects - Should reimplement as a method
steps = 100, 100
g rs = []
for dim_i in range(self.embedding.shape[1]):
m, M = np.min(self.embedding[:, dim_i]), np.max(self.embedding[:, dim_i])
m = m - 0.025 * np.abs(M - m)
M = M + 0.025 * np.abs(M - m)
gr = np.linspace(m, M, steps[dim_i])
grs.append(gr)
meshes_tuple = np.meshgrid(*grs)
gridpoints_coordinates = np.vstack([i.flat for i in meshes_tuple]).T
nn = NearestNeighbors()
nn.fit(self.embedding)
dist, ixs = nn.kneighbors(gridpoints_coordinates, 1)
diag_step_dist = np.sqrt((meshes_tuple[0][0,0] - meshes_tuple[0][0,1])**2 + (meshes_tuple[1][0,0] - meshes_tuple[1][1,0])**2)
min_dist = diag_step_dist / 2
ixs = ixs[dist < min_dist]
gridpoints_coordinates = gridpoints_coordinates[dist.flat[:]
Code Availability：
https://github.com/morris-lab/CellOracle