making genie3 work when genes are not expressed

jkobject · Nov 13, 2024 · 7ecd734 · 7ecd734
1 parent f37a7f9
commit 7ecd734
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/Makefile b/Makefile
@@ -65,6 +65,7 @@ virtualenv:       ## Create a virtual environment.
 	@source .venv/bin/activate
 	@make install
 	@echo "!!! Please run 'source .venv/bin/activate' to enable the environment !!!"
+
 
 .PHONY: release
 release:          ## Create a new tag for release.

diff --git a/bengrn/base.py b/bengrn/base.py
@@ -715,9 +715,9 @@ def compute_genie3(
         GRNAnnData: The Gene Regulatory Network data computed using the GENIE3 algorithm.
     """
     mat = np.asarray(adata.X.toarray() if issparse(adata.X) else adata.X)
-    names = adata.var_names[mat.sum(0) > 0].tolist()
-    var = adata.var[mat.sum(0) > 0]
-    mat = mat[:, mat.sum(0) > 0]
+    names = adata.var_names.tolist()  # [mat.sum(0) > 0].tolist()
+    var = adata.var  # [mat.sum(0) > 0]
+    # mat = mat[:, mat.sum(0) > 0]
     VIM = GENIE3(mat, gene_names=names, nthreads=nthreads, ntrees=ntrees, **kwargs)
     grn = GRNAnnData(grn=VIM, X=mat, var=var, obs=adata.obs)
     grn.var_names = grn.var["symbol"]