From e1bfb4644c1cf777f6d1cadebd5913453a097b06 Mon Sep 17 00:00:00 2001
From: Sergei Rybakov <koncopd@gmail.com>
Date: Mon, 12 Jul 2021 15:27:16 +0200
Subject: [PATCH] compare_abs argument in filter_rank_genes_groups (#1649)

* compare_abs

* test compare_abs

* add to release notes
---
 docs/release-notes/1.9.0.rst                  |  4 +
 scanpy/tests/test_filter_rank_genes_groups.py | 83 +++++++++++++++++++
 scanpy/tools/_rank_genes_groups.py            |  7 +-
 3 files changed, 93 insertions(+), 1 deletion(-)

diff --git a/docs/release-notes/1.9.0.rst b/docs/release-notes/1.9.0.rst
index 77c9e57f61..2ac7b6b51c 100644
--- a/docs/release-notes/1.9.0.rst
+++ b/docs/release-notes/1.9.0.rst
@@ -1,2 +1,6 @@
 1.9.0 :small:`the future`
 ~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Features
+
+- :func:`~scanpy.tl.filter_rank_genes_groups` now allows to filter with absolute values of log fold change :pr:`1649` :smaller:`S Rybakov`
diff --git a/scanpy/tests/test_filter_rank_genes_groups.py b/scanpy/tests/test_filter_rank_genes_groups.py
index 91aff2d27c..b6d7bb474c 100644
--- a/scanpy/tests/test_filter_rank_genes_groups.py
+++ b/scanpy/tests/test_filter_rank_genes_groups.py
@@ -34,6 +34,71 @@
     ]
 )
 
+names_compare_abs = np.array(
+    [
+        [
+            'CD3D',
+            'ITM2A',
+            'HLA-DRB1',
+            'CCL5',
+            'HLA-DPA1',
+            'nan',
+            'CD79A',
+            'nan',
+            'NKG7',
+            'LYZ',
+        ],
+        [
+            'HLA-DPA1',
+            'nan',
+            'CD3D',
+            'NKG7',
+            'HLA-DRB1',
+            'AIF1',
+            'CD79B',
+            'nan',
+            'GNLY',
+            'CST3',
+        ],
+        [
+            'nan',
+            'PSAP',
+            'CD74',
+            'CST7',
+            'CD74',
+            'PSAP',
+            'FCER1G',
+            'SNHG7',
+            'CD7',
+            'HLA-DRA',
+        ],
+        [
+            'IL32',
+            'nan',
+            'HLA-DRB5',
+            'GZMA',
+            'HLA-DRB5',
+            'LST1',
+            'nan',
+            'nan',
+            'CTSW',
+            'HLA-DRB1',
+        ],
+        [
+            'nan',
+            'FCER1G',
+            'HLA-DPB1',
+            'CTSW',
+            'HLA-DPB1',
+            'TYROBP',
+            'TYROBP',
+            'S100A10',
+            'GZMB',
+            'HLA-DPA1',
+        ],
+    ]
+)
+
 
 def test_filter_rank_genes_groups():
     adata = pbmc68k_reduced()
@@ -72,3 +137,21 @@ def test_filter_rank_genes_groups():
         names_no_reference,
         np.array(adata.uns['rank_genes_groups_filtered']['names'].tolist()),
     )
+
+    # test compare_abs
+    rank_genes_groups(
+        adata, 'bulk_labels', method='wilcoxon', pts=True, rankby_abs=True, n_genes=5
+    )
+
+    filter_rank_genes_groups(
+        adata,
+        compare_abs=True,
+        min_in_group_fraction=-1,
+        max_out_group_fraction=1,
+        min_fold_change=3.1,
+    )
+
+    assert np.array_equal(
+        names_compare_abs,
+        np.array(adata.uns['rank_genes_groups_filtered']['names'].tolist()),
+    )
diff --git a/scanpy/tools/_rank_genes_groups.py b/scanpy/tools/_rank_genes_groups.py
index 2e3269d6c2..c1c27320e7 100644
--- a/scanpy/tools/_rank_genes_groups.py
+++ b/scanpy/tools/_rank_genes_groups.py
@@ -670,9 +670,10 @@ def filter_rank_genes_groups(
     min_in_group_fraction=0.25,
     min_fold_change=1,
     max_out_group_fraction=0.5,
+    compare_abs=False,
 ) -> None:
     """\
-    Filters out genes based on fold change and fraction of genes expressing the
+    Filters out genes based on log fold change and fraction of genes expressing the
     gene within and outside the `groupby` categories.
 
     See :func:`~scanpy.tl.rank_genes_groups`.
@@ -693,6 +694,8 @@ def filter_rank_genes_groups(
     min_in_group_fraction
     min_fold_change
     max_out_group_fraction
+    compare_abs
+        If `True`, compare absolute values of log fold change with `min_fold_change`.
 
     Returns
     -------
@@ -794,6 +797,8 @@ def filter_rank_genes_groups(
                 / (expm1_func(mean_out_cluster) + 1e-9)
             )
 
+    if compare_abs:
+        fold_change_matrix = fold_change_matrix.abs()
     # filter original_matrix
     gene_names = gene_names[
         (fraction_in_cluster_matrix > min_in_group_fraction)