Merge pull request #23 from abearab/dev

update plot_top_DEG_violinplot function
abearab · Jan 7, 2025 · efc3376 · efc3376
2 parents ce87ac5 + 47ff25c
commit efc3376
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diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "scez"
-version = "0.1.1"
+version = "0.1.2"
 authors = [
 	"Abe Arab <abarbiology@gmail.com>"
 ]

diff --git a/scez/diffexp.py b/scez/diffexp.py
@@ -136,7 +136,8 @@ def plot_volcano(df, title=None, labels=None, n_genes=False, side='both',
         plt.show()
 
 
-def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
+def plot_top_DEG_violinplot(adata, df, layer=None, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
+
     label_font_size = 9 * font_scale
     title_font_size = 10 * font_scale
 
@@ -167,11 +168,11 @@ def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, s
         selected_genes = df.nlargest(n_genes, '-log10(pvalue)')
 
     # Filter the single-cell dataset for the selected genes
-    subset_adata = adata[:, selected_genes.index]
+    subset_adata = adata[:, selected_genes.index].copy()
     subset_adata.var.index = subset_adata.var.index.str.split('_').str[0]
 
     # Convert the subset of adata to a DataFrame
-    subset_df = subset_adata.to_df()
+    subset_df = subset_adata.to_df(layer=layer)
 
     # Merge the DataFrame with .obs to include the 'sample' information
     merged_df = pd.merge(subset_df, adata.obs[['sample']], left_index=True, right_index=True)