From 53ad9ba43ae668812b6b569d1e74a699ce2768f1 Mon Sep 17 00:00:00 2001
From: Blampey Quentin <quentin.blampey@centralesupelec.fr>
Date: Mon, 8 Apr 2024 15:36:12 +0200
Subject: [PATCH] rename compensate

---
 CHANGELOG.md           | 4 ++++
 docs/api/preprocess.md | 2 +-
 pyproject.toml         | 2 +-
 scyan/preprocess.py    | 7 ++++---
 4 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index def0459..a424ed8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+## [1.6.1] - 2024-04-08
+
+Rename `correct_spillover` -> `compensate`
+
 ## [1.6.0] - 2024-04-08
 
 ### Changed
diff --git a/docs/api/preprocess.md b/docs/api/preprocess.md
index df448f3..bd22729 100644
--- a/docs/api/preprocess.md
+++ b/docs/api/preprocess.md
@@ -18,6 +18,6 @@
     options:
       show_root_heading: true
 
-::: scyan.preprocess.correct_spillover
+::: scyan.preprocess.compensate
     options:
       show_root_heading: true
diff --git a/pyproject.toml b/pyproject.toml
index 329b8bc..e9c40da 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "scyan"
-version = "1.6.0"
+version = "1.6.1"
 description = "Single-cell Cytometry Annotation Network"
 documentation = "https://mics-lab.github.io/scyan/"
 homepage = "https://mics-lab.github.io/scyan/"
diff --git a/scyan/preprocess.py b/scyan/preprocess.py
index b3e9ebd..9487fb6 100644
--- a/scyan/preprocess.py
+++ b/scyan/preprocess.py
@@ -216,8 +216,8 @@ def subsample(adata: AnnData, n_obs: int) -> AnnData:
     return adata[indices]
 
 
-def correct_spillover(adata: AnnData, key_added: Optional[str] = None):
-    """Use the spillover matrix in `adata.varp["spillover_matrix"]` to correct spillover
+def compensate(adata: AnnData, key_added: Optional[str] = None):
+    """Use the spillover matrix in `adata.varp["spillover_matrix"]` to correct spillover from `adata.X`
 
     Args:
         adata: An `AnnData` object
@@ -231,7 +231,8 @@ def correct_spillover(adata: AnnData, key_added: Optional[str] = None):
     ):
         log.warn("It is recommended to apply spillover only on raw data (unprocessed)")
 
-    corrected = adata.X @ adata.varp["spillover_matrix"].T
+    S = adata.varp["spillover_matrix"]
+    corrected = np.linalg.solve(S, adata.X.T).T
 
     if key_added is None:
         adata.X = corrected