Updated the notebook

malariagen · Jun 20, 2024 · 1efc4bc · 1efc4bc
1 parent b0822d1
commit 1efc4bc
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Showing 2 changed files with 8 additions and 9 deletions.
diff --git a/malariagen_data/anoph/fst.py b/malariagen_data/anoph/fst.py
@@ -501,13 +501,12 @@ def plot_pairwise_average_fst(
             col = fst_df.iloc[index_key]["cohort2"]
             fst = fst_df.iloc[index_key]["fst"]
             fig_df[index][col] = fst
-            if annotation:
-                if annotation == "standard error":
-                    se = fst_df.iloc[index_key]["se"]
-                    fig_df[col][index] = se
-                elif annotation == "Z score":
-                    zs = fst_df.iloc[index_key]["fst"] / fst_df.iloc[index_key]["se"]
-                    fig_df[col][index] = zs
+            if annotation == "standard error":
+                se = fst_df.iloc[index_key]["se"]
+                fig_df[col][index] = se
+            elif annotation == "Z score":
+                zs = fst_df.iloc[index_key]["fst"] / fst_df.iloc[index_key]["se"]
+                fig_df[col][index] = zs
             else:
                 fig_df.loc[index, col] = fst
 

diff --git a/notebooks/plot_pairwise_average_fst.ipynb b/notebooks/plot_pairwise_average_fst.ipynb
@@ -94,7 +94,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ag3.plot_pairwise_average_fst(pairwise_fst_df, annotate_se=True)"
+    "ag3.plot_pairwise_average_fst(pairwise_fst_df, annotation=\"standard error\")"
    ]
   },
   {
@@ -104,7 +104,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ag3.plot_pairwise_average_fst(pairwise_fst_df, annotate_se=False)"
+    "ag3.plot_pairwise_average_fst(pairwise_fst_df, annotation=\"Z score\")"
    ]
   },
   {