phlower.tl.diffusionGraph

phlower.tl.diffusionGraph(X, roots, k=11, npc=None, ndc=40, s=1, j=7, lmda=0.0001, sigma=None, verbose=False, lstsq_method='lstsq')

Parameters

X: numpy array

column observations,row features

roots: list

list of bool values if they are root nodes

k: int

number of nearest neighbors for diffusion map

npc: int

number of principal components using

ndc: int

number of diffusion components using

s: int

number of stepes for diffusion map random walk(default 1)

lmda: float

regularization parameter for ddhodge(default 1e-4)

sigma: float

sigma for gaussian kernel(default None)

verbose: bool

print out progress(default False)

lstsq_method: str

method for least square solver, “lstsq” or “lsqr”, “lsmr” (default “lstsq”)

Return

dic: dict

d[‘g’]: The diffusion graph d[‘A’]: Graph full adjacency matrix d[‘W’]: Diffusion Distances d[‘psi’]: Diffusion Map right eigenvectors d[‘phi’]: Diffusion Map left eigenvectors d[‘eig’]: Diffusion Map eigenvalues d[‘dm’]: dimension reduction input of diffusion map