scverse · ivirshup · Feb 10, 2021 · Jan 30, 2021 · Jan 30, 2021 · Jan 31, 2021
diff --git a/docs/release-latest.rst b/docs/release-latest.rst
@@ -4,6 +4,13 @@
 Version 1.7
 -----------
 
+1.7.1 :small:`the future`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Bugfixes
+
+- :func:`~scanpy.tl.dendrogram` use `1 - correlation` as distance matrix to compute the dendrogram :pr`1614` :smaller:`F Ramirez`
+
 1.7.0 :small:`2021-02-03`
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/scanpy/get/__init__.py b/scanpy/get/__init__.py
@@ -1,4 +1,5 @@
 # Public
 from .get import rank_genes_groups_df, obs_df, var_df
+
 # Private
 from .get import _get_obs_rep, _set_obs_rep
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)