phlower.tl.run_palantir_fdl

phlower.tl.run_palantir_fdl(mtx, cell_names=None, verbose=True, iterations=500, device='cpu', knn=30, alpha=0, edgeWeightInfluence=0.5, scalingRatio=2.0, gravity=1.0, random_state=2022, n_components=10, outboundAttractionDistribution=False, strongGravityMode=False)

“ Function to compute force directed layout from the affinity_matrix adjusted from: https://github.com/dpeerlab/Harmony/blob/master/src/harmony/plot.py :param affinity_matrix: Sparse matrix representing affinities between cells :param cell_names: pandas Series object with cell names :param verbose: Verbosity for force directed layout computation :param iterations: Number of iterations used by ForceAtlas :return: Pandas data frame representing the force directed layout