Merge pull request #60 from demian1/main

updated docs
saezlab · Jul 30, 2023 · e9402a5 · e9402a5
2 parents 459b235 + c39ede5
commit e9402a5
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Showing 3 changed files with 8 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
 -------