scverse · ivirshup · Feb 10, 2021 · Jan 30, 2021 · Jan 30, 2021 · Jan 31, 2021
diff --git a/scanpy/plotting/_anndata.py b/scanpy/plotting/_anndata.py
@@ -1007,6 +1007,7 @@ def heatmap(
                 # if colors are not found, assign a new palette
                 # and save it using the same code for embeddings
                 from ._tools.scatterplots import _get_palette
+
                 _get_palette(adata, groupby)
             groupby_colors = adata.uns[groupby + "_colors"]
         else:
@@ -1212,7 +1213,7 @@ def heatmap(
 
         kwds.setdefault('interpolation', 'nearest')
         im = heatmap_ax.imshow(obs_tidy.T.values, aspect='auto', **kwds)
-        heatmap_ax.set_xlim(0 - 0.5, obs_tidy.shape[0] -0.5)
+        heatmap_ax.set_xlim(0 - 0.5, obs_tidy.shape[0] - 0.5)
         heatmap_ax.set_ylim(obs_tidy.shape[1] - 0.5, -0.5)
         heatmap_ax.tick_params(axis='x', bottom=False, labelbottom=False)
         heatmap_ax.set_xlabel('')
@@ -1242,7 +1243,7 @@ def heatmap(
             heatmap_ax.vlines(
                 line_positions,
                 -0.5,
-                len(var_names) -0.5,
+                len(var_names) - 0.5,
                 lw=1,
                 color='black',
                 zorder=10,

diff --git a/scanpy/tests/_images/correlation.png b/scanpy/tests/_images/correlation.png
diff --git a/scanpy/tests/_images/dendrogram.png b/scanpy/tests/_images/dendrogram.png
diff --git a/scanpy/tests/_images/master_dotplot.png b/scanpy/tests/_images/master_dotplot.png
diff --git a/scanpy/tests/_images/master_dotplot3.png b/scanpy/tests/_images/master_dotplot3.png
diff --git a/scanpy/tests/_images/master_dotplot_dict.png b/scanpy/tests/_images/master_dotplot_dict.png
diff --git a/scanpy/tests/_images/master_dotplot_gene_symbols.png b/scanpy/tests/_images/master_dotplot_gene_symbols.png
diff --git a/scanpy/tests/_images/master_dotplot_std_scale_group.png b/scanpy/tests/_images/master_dotplot_std_scale_group.png
diff --git a/scanpy/tests/_images/master_dotplot_std_scale_var.png b/scanpy/tests/_images/master_dotplot_std_scale_var.png
diff --git a/scanpy/tests/_images/master_heatmap_var_as_dict.png b/scanpy/tests/_images/master_heatmap_var_as_dict.png
diff --git a/scanpy/tests/_images/master_matrixplot_std_scale_var_dict.png b/scanpy/tests/_images/master_matrixplot_std_scale_var_dict.png
diff --git a/scanpy/tests/_images/master_multiple_plots.png b/scanpy/tests/_images/master_multiple_plots.png
diff --git a/scanpy/tests/_images/master_ranked_genes_dotplot.png b/scanpy/tests/_images/master_ranked_genes_dotplot.png
diff --git a/scanpy/tests/_images/master_ranked_genes_dotplot_logfoldchange.png b/scanpy/tests/_images/master_ranked_genes_dotplot_logfoldchange.png
diff --git a/scanpy/tests/_images/master_ranked_genes_heatmap.png b/scanpy/tests/_images/master_ranked_genes_heatmap.png
diff --git a/scanpy/tests/_images/master_ranked_genes_heatmap_swap_axes.png b/scanpy/tests/_images/master_ranked_genes_heatmap_swap_axes.png
diff --git a/scanpy/tests/_images/master_ranked_genes_matrixplot.png b/scanpy/tests/_images/master_ranked_genes_matrixplot.png
diff --git a/scanpy/tests/_images/master_ranked_genes_matrixplot_swap_axes.png b/scanpy/tests/_images/master_ranked_genes_matrixplot_swap_axes.png
diff --git a/scanpy/tests/_images/master_ranked_genes_stacked_violin.png b/scanpy/tests/_images/master_ranked_genes_stacked_violin.png
diff --git a/scanpy/tests/_images/master_ranked_genes_tracksplot.png b/scanpy/tests/_images/master_ranked_genes_tracksplot.png
diff --git a/scanpy/tests/_images/master_stacked_violin.png b/scanpy/tests/_images/master_stacked_violin.png
diff --git a/scanpy/tests/_images/master_stacked_violin_gene_symbols.png b/scanpy/tests/_images/master_stacked_violin_gene_symbols.png
diff --git a/scanpy/tests/_images/master_stacked_violin_std_scale_var_dict.png b/scanpy/tests/_images/master_stacked_violin_std_scale_var_dict.png
diff --git a/scanpy/tests/_images/master_tsne.png b/scanpy/tests/_images/master_tsne.png
diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
@@ -133,10 +133,12 @@ def dendrogram(
     mean_df = rep_df.groupby(level=0).mean()
 
     import scipy.cluster.hierarchy as sch
+    from scipy.spatial import distance
 
     corr_matrix = mean_df.T.corr(method=cor_method)
+    corr_condensed = distance.squareform(1 - corr_matrix)
     z_var = sch.linkage(
-        corr_matrix, method=linkage_method, optimal_ordering=optimal_ordering
+        corr_condensed, method=linkage_method, optimal_ordering=optimal_ordering
     )
     dendro_info = sch.dendrogram(z_var, labels=list(categories), no_plot=True)