diff --git a/pertpy/tools/_coda/_base_coda.py b/pertpy/tools/_coda/_base_coda.py index e600046d..4bb42433 100644 --- a/pertpy/tools/_coda/_base_coda.py +++ b/pertpy/tools/_coda/_base_coda.py @@ -1864,9 +1864,6 @@ def plot_draw_tree( # pragma: no cover >>> ) >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42) >>> tasccoda.plot_draw_tree(mdata, tree="lineage") - - Preview: - #TODO: Add preview """ try: from ete3 import CircleFace, NodeStyle, TextFace, Tree, TreeStyle, faces @@ -1956,9 +1953,6 @@ def plot_draw_effects( # pragma: no cover >>> ) >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42) >>> pt.pl.coda.draw_effects(mdata, covariate="Health[T.Inflamed]", tree="lineage") - - Preview: - #TODO: Add preview """ try: from ete3 import CircleFace, NodeStyle, TextFace, Tree, TreeStyle, faces @@ -2150,9 +2144,6 @@ def plot_effects_umap( # pragma: no cover >>> "effect_df_condition[T.Hpoly.Day10]"], >>> cluster_key="nsbm_level_1", >>> ) - - Preview: - #TODO: Add preview """ # TODO: Add effect_name parameter and cluster_key and test the example data_rna = data[modality_key_1] diff --git a/pertpy/tools/_mixscape.py b/pertpy/tools/_mixscape.py index 16f0cbff..93dae15f 100644 --- a/pertpy/tools/_mixscape.py +++ b/pertpy/tools/_mixscape.py @@ -443,7 +443,7 @@ def _get_perturbation_markers( min_de_genes: float, logfc_threshold: float, ) -> dict[tuple, np.ndarray]: - """determine gene sets across all splits/groups through differential gene expression + """Determine gene sets across all splits/groups through differential gene expression Args: adata: :class:`~anndata.AnnData` object @@ -695,9 +695,6 @@ def plot_perturbscore( # pragma: no cover perturbation_type: Specify type of CRISPR perturbation expected for labeling mixscape classifications. Defaults to `KO`. - Returns: - None. - Examples: Visualizing the perturbation scores for the cells in a dataset: