Misc fixes

CSOgroup · Aug 6, 2024 · fcc8007 · fcc8007
1 parent bb9fff2
commit fcc8007
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Showing 5 changed files with 9 additions and 6 deletions.
diff --git a/src/cellcharter/gr/_build.py b/src/cellcharter/gr/_build.py
@@ -120,9 +120,9 @@ def remove_intra_cluster_links(
 
     # ToDo: compute inter_cluster_mask only on conns and apply mask to both matrices
     for matrix in [conns, dists]:
-        target_clusters = np.array(adata.obs[cluster_key][matrix.indices])
+        target_clusters = np.array(adata.obs[cluster_key].iloc[matrix.indices])
         source_clusters = np.array(
-            adata.obs[cluster_key][np.repeat(np.arange(matrix.indptr.shape[0] - 1), np.diff(matrix.indptr))]
+            adata.obs[cluster_key].iloc[np.repeat(np.arange(matrix.indptr.shape[0] - 1), np.diff(matrix.indptr))]
         )
 
         inter_cluster_mask = (source_clusters != target_clusters).astype(int)

diff --git a/src/cellcharter/gr/_group.py b/src/cellcharter/gr/_group.py
@@ -26,7 +26,8 @@ def _enrichment(observed, expected, log=True):
     enrichment = observed.div(expected, axis="index", level=0)
 
     if log:
-        enrichment = np.log2(enrichment)
+        with np.errstate(divide="ignore"):
+            enrichment = np.log2(enrichment)
     enrichment = enrichment.fillna(enrichment.min())
     return enrichment
 

diff --git a/src/cellcharter/pl/_shape.py b/src/cellcharter/pl/_shape.py
@@ -135,7 +135,7 @@ def boundaries(
         "cells": sd.models.ShapesModel.parse(cell_circles),
     }
 
-    sdata = sd.SpatialData(shapes=shapes, table=table)
+    sdata = sd.SpatialData(shapes=shapes, tables=table)
 
     ax = plt.gca()
     if show_cells:
@@ -151,7 +151,7 @@ def boundaries(
             sdata.pl.render_shapes(elements="cells", color=component_key).pl.show(ax=ax, legend_loc=None)
 
     sdata.pl.render_shapes(
-        elements="clusters",
+        element="clusters",
         color=component_key,
         fill_alpha=alpha_boundary,
     ).pl.show(ax=ax)

diff --git a/src/cellcharter/pl/_utils.py b/src/cellcharter/pl/_utils.py
@@ -96,7 +96,7 @@ def _heatmap(
         )
 
     row_order = row_order[::-1]
-    row_labels = adata.obs[key][row_order]
+    row_labels = adata.obs[key].iloc[row_order]
     col_labels = adata.var_names[col_order]
 
     data = adata[row_order, col_order].copy().X

diff --git a/tests/plotting/test_group.py b/tests/plotting/test_group.py
@@ -1,3 +1,4 @@
+import matplotlib.pyplot as plt
 import pytest
 import squidpy as sq
 
@@ -75,6 +76,7 @@ def test_params(
             alpha=alpha,
             edgecolor=edgecolor,
         )
+        plt.close()
 
     def test_no_pvalues(self):
         # If the enrichment data is not present, it should raise an error