From 21a486e5b078111be67b598d2e3f6e6a6e93dc61 Mon Sep 17 00:00:00 2001
From: Wojciech Lason <wojciech.lason@ndm.ox.ac.uk>
Date: Tue, 20 Aug 2024 16:53:11 +0100
Subject: [PATCH] Modified batch_correct_mofa.py to add lowmem parameter

---
 .../pipeline_integration/pipeline.yml         |  1 +
 panpipes/python_scripts/batch_correct_mofa.py | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)

diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml
index a8693636..0445dcfe 100644
--- a/panpipes/panpipes/pipeline_integration/pipeline.yml
+++ b/panpipes/panpipes/pipeline_integration/pipeline.yml
@@ -197,6 +197,7 @@ multimodal:
   mofa:
     modalities: rna,prot,atac
     filter_by_hvg: True
+    lowmem: True
     n_factors: 10
     n_iterations: 1000
     convergence_mode: fast
diff --git a/panpipes/python_scripts/batch_correct_mofa.py b/panpipes/python_scripts/batch_correct_mofa.py
index b9300df0..afc4655c 100644
--- a/panpipes/python_scripts/batch_correct_mofa.py
+++ b/panpipes/python_scripts/batch_correct_mofa.py
@@ -95,6 +95,21 @@
 L.info("Intersecting modality obs before running mofa")
 mu.pp.intersect_obs(tmp)
 
+
+if check_for_bool(params["multimodal"]["MultiVI"]["lowmem"]):
+    L.info("Running in low memory mode. Calculating and subsetting ATAC to top 25k HVF")
+    atac = tmp.mod['atac']
+    
+    sc.pp.highly_variable_genes(atac, n_top_genes=25000)
+    atac = atac[:, atac.var.highly_variable].copy()
+    
+    tmp.mod['atac'] = atac.copy()
+    del atac
+
+    tmp.update()
+
+gc.collect()
+
 mofa_kwargs={}
 #expected args:
 # n_factors: 10
@@ -106,6 +121,7 @@
 
 mofa_kwargs = params['multimodal']['mofa']
 del mofa_kwargs['modalities']
+del mofa_kwargs['lowmem']
 
 if mofa_kwargs['filter_by_hvg']:
     mofa_kwargs['use_var'] = "highly_variable"
@@ -115,6 +131,9 @@
             tmp[mod].var["highly_variable"] = True
         
     tmp.update()
+else:
+    del mofa_kwargs['filter_by_hvg']
+    mofa_kwargs['use_var'] = None