How to use the scvelo.logging.switch_verbosity function in scvelo

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github theislab / scvelo / scvelo / preprocessing / neighbors.py View on Github external
neighbors.distances, neighbors.connectivities = compute_connectivities_umap(
            neighbors.knn_indices, knn_distances, X.shape[0], n_neighbors=n_neighbors
        )

    elif method == "hnsw":
        X = adata.X if use_rep == "X" else adata.obsm[use_rep]
        neighbors = FastNeighbors(n_neighbors=n_neighbors, num_threads=num_threads)
        neighbors.fit(
            X if n_pcs is None else X[:, :n_pcs],
            metric=metric,
            random_state=random_state,
            **metric_kwds,
        )

    else:
        logg.switch_verbosity("off", module="scanpy")
        with warnings.catch_warnings():  # ignore numba warning (umap/issues/252)
            warnings.simplefilter("ignore")
            neighbors = Neighbors(adata)
            neighbors.compute_neighbors(
                n_neighbors=n_neighbors,
                knn=knn,
                n_pcs=n_pcs,
                method=method,
                use_rep=None if use_rep == "X_pca" else use_rep,
                random_state=random_state,
                metric=metric,
                metric_kwds=metric_kwds,
                write_knn_indices=True,
            )
        logg.switch_verbosity("on", module="scanpy")
github theislab / scvelo / scvelo / tools / rank_velocity_genes.py View on Github external
tmp_filter &= (adata.var['fit_likelihood'] > min_likelihood)

    from .. import AnnData
    vdata = AnnData(adata.layers[vkey][:, tmp_filter])
    vdata.obs = adata.obs.copy()
    vdata.var = adata.var[tmp_filter].copy()

    if 'highly_variable' in vdata.var.keys():
        vdata.var['highly_variable'] = np.array(vdata.var['highly_variable'], dtype=bool)

    import scanpy as sc
    logg.switch_verbosity('off', module='scanpy')
    sc.pp.pca(vdata, n_comps=20, svd_solver='arpack')
    sc.pp.neighbors(vdata, n_pcs=20)
    sc.tl.louvain(vdata, resolution=.7 if resolution is None else resolution)
    logg.switch_verbosity('on', module='scanpy')

    if sort_by == 'velocity_pseudotime' and sort_by not in adata.obs.keys():
        velocity_pseudotime(adata, vkey=vkey)
    if sort_by in vdata.obs.keys():
        vc = vdata.obs['louvain']
        vc_cats = vc.cat.categories
        mean_times = [np.mean(vdata.obs[sort_by][vc == cat]) for cat in vc_cats]
        vdata.obs['louvain'].cat.reorder_categories(vc_cats[np.argsort(mean_times)], inplace=True)

    if isinstance(match_with, str) and match_with in adata.obs.keys():
        from .utils import most_common_in_list
        vc = vdata.obs['louvain']
        cats_nums = {cat: 0 for cat in adata.obs[match_with].cat.categories}
        for i, cat in enumerate(vc.cat.categories):
            cells_in_cat = np.where(vc == cat)[0]
            new_cat = most_common_in_list(adata.obs[match_with][cells_in_cat])
github theislab / scvelo / scvelo / tools / velocity_confidence.py View on Github external
data, adata_subset=None, fraction=0.5, vkey="velocity", copy=False
):
    adata = data.copy() if copy else data

    if adata_subset is None:
        from ..preprocessing.moments import moments
        from ..preprocessing.neighbors import neighbors
        from .velocity import velocity

        logg.switch_verbosity("off")
        adata_subset = adata.copy()
        subset = random_subsample(adata_subset, fraction=fraction, return_subset=True)
        neighbors(adata_subset)
        moments(adata_subset)
        velocity(adata_subset, vkey=vkey)
        logg.switch_verbosity("on")
    else:
        subset = adata.obs_names.isin(adata_subset.obs_names)

    V = adata[subset].layers[vkey]
    V_subset = adata_subset.layers[vkey]

    score = np.nan * (subset == False)
    score[subset] = prod_sum_var(V, V_subset) / (norm(V) * norm(V_subset))
    adata.obs[f"{vkey}_score_robustness"] = score

    return adata_subset if copy else None
github theislab / scvelo / scvelo / preprocessing / neighbors.py View on Github external
logg.switch_verbosity("off", module="scanpy")
        with warnings.catch_warnings():  # ignore numba warning (umap/issues/252)
            warnings.simplefilter("ignore")
            neighbors = Neighbors(adata)
            neighbors.compute_neighbors(
                n_neighbors=n_neighbors,
                knn=knn,
                n_pcs=n_pcs,
                method=method,
                use_rep=None if use_rep == "X_pca" else use_rep,
                random_state=random_state,
                metric=metric,
                metric_kwds=metric_kwds,
                write_knn_indices=True,
            )
        logg.switch_verbosity("on", module="scanpy")

    adata.uns["neighbors"] = {}
    try:
        adata.obsp["distances"] = neighbors.distances
        adata.obsp["connectivities"] = neighbors.connectivities
        adata.uns["neighbors"]["connectivities_key"] = "connectivities"
        adata.uns["neighbors"]["distances_key"] = "distances"
    except:
        adata.uns["neighbors"]["distances"] = neighbors.distances
        adata.uns["neighbors"]["connectivities"] = neighbors.connectivities

    if hasattr(neighbors, "knn_indices"):
        adata.uns["neighbors"]["indices"] = neighbors.knn_indices
    adata.uns["neighbors"]["params"] = {
        "n_neighbors": n_neighbors,
        "method": method,
github theislab / scvelo / scvelo / tools / rank_velocity_genes.py View on Github external
min_dispersion = np.percentile(dispersions, 20)
        tmp_filter &= (dispersions > min_dispersion)

    if 'fit_likelihood' in adata.var.keys() and min_likelihood is not None:
        tmp_filter &= (adata.var['fit_likelihood'] > min_likelihood)

    from .. import AnnData
    vdata = AnnData(adata.layers[vkey][:, tmp_filter])
    vdata.obs = adata.obs.copy()
    vdata.var = adata.var[tmp_filter].copy()

    if 'highly_variable' in vdata.var.keys():
        vdata.var['highly_variable'] = np.array(vdata.var['highly_variable'], dtype=bool)

    import scanpy as sc
    logg.switch_verbosity('off', module='scanpy')
    sc.pp.pca(vdata, n_comps=20, svd_solver='arpack')
    sc.pp.neighbors(vdata, n_pcs=20)
    sc.tl.louvain(vdata, resolution=.7 if resolution is None else resolution)
    logg.switch_verbosity('on', module='scanpy')

    if sort_by == 'velocity_pseudotime' and sort_by not in adata.obs.keys():
        velocity_pseudotime(adata, vkey=vkey)
    if sort_by in vdata.obs.keys():
        vc = vdata.obs['louvain']
        vc_cats = vc.cat.categories
        mean_times = [np.mean(vdata.obs[sort_by][vc == cat]) for cat in vc_cats]
        vdata.obs['louvain'].cat.reorder_categories(vc_cats[np.argsort(mean_times)], inplace=True)

    if isinstance(match_with, str) and match_with in adata.obs.keys():
        from .utils import most_common_in_list
        vc = vdata.obs['louvain']
github theislab / scvelo / scvelo / tools / velocity_confidence.py View on Github external
def score_robustness(
    data, adata_subset=None, fraction=0.5, vkey="velocity", copy=False
):
    adata = data.copy() if copy else data

    if adata_subset is None:
        from ..preprocessing.moments import moments
        from ..preprocessing.neighbors import neighbors
        from .velocity import velocity

        logg.switch_verbosity("off")
        adata_subset = adata.copy()
        subset = random_subsample(adata_subset, fraction=fraction, return_subset=True)
        neighbors(adata_subset)
        moments(adata_subset)
        velocity(adata_subset, vkey=vkey)
        logg.switch_verbosity("on")
    else:
        subset = adata.obs_names.isin(adata_subset.obs_names)

    V = adata[subset].layers[vkey]
    V_subset = adata_subset.layers[vkey]

    score = np.nan * (subset == False)
    score[subset] = prod_sum_var(V, V_subset) / (norm(V) * norm(V_subset))
    adata.obs[f"{vkey}_score_robustness"] = score