From c39ede5167debc3cdd0d5ffbe0981032c651517a Mon Sep 17 00:00:00 2001 From: demian1 Date: Mon, 24 Jul 2023 10:43:29 +0200 Subject: [PATCH] updated docs --- decoupler/plotting.py | 1 + decoupler/utils_anndata.py | 4 ++-- docs/source/api.rst | 5 +++++ 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/decoupler/plotting.py b/decoupler/plotting.py index a375caf..87447dd 100644 --- a/decoupler/plotting.py +++ b/decoupler/plotting.py @@ -1505,6 +1505,7 @@ def _check_assoc_plot_intputs(data, associations, cols, uns_key, obsm_key, use_X def plot_associations(data, uns_key, associations = None, cols = None, obs_annotation_cols = None, obsm_key=None, use_X = False, layer= None, stat_col = 'p_adj', titles = ['Scores', 'Stats'], scores_kwargs = {}, stats_kwargs = {}): """ Create a composite plot displaying association results between scores (bottom) and summary statistics (top) using a ClusterMap. + Requires PyComplexHeatmap to be installed. Parameters: diff --git a/decoupler/utils_anndata.py b/decoupler/utils_anndata.py index a236a88..693dda4 100644 --- a/decoupler/utils_anndata.py +++ b/decoupler/utils_anndata.py @@ -972,9 +972,9 @@ def _check_anova_inputs(data, obs_keys = None, obsm_key=None, use_X = False, lay def get_metadata_associations(data, obs_keys = None, obsm_key=None, use_X = False, layer = None, uns_key = None, inplace = False, alpha = 0.05, method = 'fdr_bh'): """ - Associate the data to sample metadata using ANOVA. + Associate the data to sample metadata using ANOVA. The data can be any kind of embedding stored in a layer, obsm or X matrix. - Requires statsmodels to be installed + Requires statsmodels to be installed. Parameters ---------- diff --git a/docs/source/api.rst b/docs/source/api.rst index 6f5499b..5cbee6a 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -76,6 +76,7 @@ AnnData utils: format_contrast_results filter_by_expr filter_by_prop + get_metadata_associations Omnipath wrappers: ------------------ @@ -104,6 +105,10 @@ Plotting plot_filter_by_prop plot_volcano_df plot_targets + plot_running_score + plot_barplot_df + plot_dotplot + plot_associations Metrics -------