Fixed edgeR test

scverse · Sep 9, 2024 · 0ddfe79 · 0ddfe79
1 parent 6d1ffe8
commit 0ddfe79
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diff --git a/pertpy/tools/_differential_gene_expression/_base.py b/pertpy/tools/_differential_gene_expression/_base.py
@@ -742,7 +742,6 @@ def plot_fold_change(
         self,
         results_df: pd.DataFrame,
         *,
-        pairedby: str = None,  # TODO: Discuss how to include
         var_names: Sequence[str] = None,
         n_top_vars: int = 15,
         y_label: str = "Log2 fold change",

diff --git a/tests/tools/_differential_gene_expression/test_edger.py b/tests/tools/_differential_gene_expression/test_edger.py
@@ -7,16 +7,13 @@ def test_edger_simple(test_adata):
     1. Initialized
     2. Fitted
     3. That test_contrast returns a DataFrame with the correct number of rows
-    4. That the plot_volcano method works
     """
     method = EdgeR(adata=test_adata, design="~condition")
     method.fit()
     res_df = method.test_contrasts(method.contrast("condition", "A", "B"))
 
     assert len(res_df) == test_adata.n_vars
 
-    method.plot_volcano(res_df, save=False)
-
 
 def test_edger_complex(test_adata):
     """Check that the EdgeR method can be initialized with a different covariate name and fitted and that the test_contrast