pythonflex 0.3__tar.gz → 0.3.1__tar.gz

{pythonflex-0.3 → pythonflex-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonflex
-Version: 0.3
+Version: 0.3.1
 Summary: pythonFLEX is a benchmarking toolkit for evaluating CRISPR screen results against biological gold standards. The toolkit computes gene-level and complex-level performance metrics, helping researchers systematically assess the biological relevance and resolution of their CRISPR screening data.
 Author-email: Yasir Demirtaş <tyasird@hotmail.com>
 Requires-Python: >=3.9

{pythonflex-0.3 → pythonflex-0.3.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pythonflex"
-version = "0.3"
+version = "0.3.1"
 description = "pythonFLEX is a benchmarking toolkit for evaluating CRISPR screen results against biological gold standards. The toolkit computes gene-level and complex-level performance metrics, helping researchers systematically assess the biological relevance and resolution of their CRISPR screening data."
 readme = "README.md"
 authors = [

pythonflex-0.3.1/src/pythonflex/examples/test2.py

@@ -0,0 +1,11 @@
+#%%
+import anndata as ad
+
+adata = ad.read_h5ad(
+    "C:/Users/yd/Desktop/22mcell/GWCD4i.pseudobulk_merged.h5ad",
+    backed="r"   # read-only, disk-backed
+)
+
+#%%
+adata
+# %%

{pythonflex-0.3 → pythonflex-0.3.1}/src/pythonflex/plotting.py

@@ -58,7 +58,12 @@ def plot_precision_recall_curve(line_width=2.0, hide_minor_ticks=True):
         log.warning(f"Color map '{cmap_name}' not found. Falling back to 'tab10'.")
         cmap = get_cmap("tab10")
 
-    fig, ax = plt.subplots()
+    # Increase figure width to accommodate external legend without squashing axes
+    fig, ax = plt.subplots(figsize=(6, 4))
+    
+    # Adjust layout to make room for legend on the right
+    plt.subplots_adjust(right=0.7)
+    
     ax.set_xscale("log")
 
     # optionally hide minor ticks on the log axis
@@ -92,7 +97,7 @@ def plot_precision_recall_curve(line_width=2.0, hide_minor_ticks=True):
     ax.set(title="",
            xlabel="Number of True Positives (TP)",
            ylabel="Precision")
-    ax.legend(loc="upper right", frameon=False)
+    ax.legend(loc="upper left", bbox_to_anchor=(1.05, 1), frameon=False)
     ax.set_ylim(0, 1)
 
     # Nature style: no grid, open top/right spines
@@ -1335,7 +1340,10 @@ def plot_mpr_tp_multi(
         colors = final_colors
     
     if ax is None:
-        fig, ax = plt.subplots(figsize=(5, 4))
+        # Increase width slightly
+        fig, ax = plt.subplots(figsize=(6, 4))
+        # Reserve space for legend on right
+        plt.subplots_adjust(right=0.7)
     else:
         fig = ax.figure
     
@@ -1504,7 +1512,10 @@ def plot_mpr_complexes_multi(
         colors = final_colors
     
     if ax is None:
-        fig, ax = plt.subplots(figsize=(5, 4))
+        # Increase width slightly
+        fig, ax = plt.subplots(figsize=(6, 4))
+        # Reserve space for legend on right
+        plt.subplots_adjust(right=0.7)
     else:
         fig = ax.figure
     
@@ -1602,12 +1613,12 @@ def _add_vertical_legend(ax, dataset_names, colors, show_filters, linewidth):
     legend1 = ax.legend(
         dataset_handles, 
         dataset_names, 
-        loc="upper right",
+        loc="upper left",
         frameon=False,
         title="Dataset",
         fontsize=7,
         title_fontsize=8,
-        bbox_to_anchor=(1.0, 1.0)
+        bbox_to_anchor=(1.05, 1.0)
     )
     ax.add_artist(legend1)
     
@@ -1615,10 +1626,10 @@ def _add_vertical_legend(ax, dataset_names, colors, show_filters, linewidth):
     legend2 = ax.legend(
         filter_handles,
         filter_labels,
-        loc="upper right",
+        loc="upper left",
         frameon=False,
         fontsize=7,
-        bbox_to_anchor=(1.0, 1.0 - len(dataset_names) * 0.04 - 0.08)
+        bbox_to_anchor=(1.05, 1.0 - len(dataset_names) * 0.06 - 0.1)
     )