cytocommunity2 1.0.6__tar.gz → 1.0.7__tar.gz

{cytocommunity2-1.0.6/src/cytocommunity2.egg-info → cytocommunity2-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cytocommunity2
-Version: 1.0.6
+Version: 1.0.7
 Summary: Weakly supervised cellular-neighborhood learning for spatial omics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{cytocommunity2-1.0.6 → cytocommunity2-1.0.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cytocommunity2"
-version = "1.0.6"
+version = "1.0.7"
 description = "Weakly supervised cellular-neighborhood learning for spatial omics"
 readme = "README.md"
 requires-python = ">=3.10"

{cytocommunity2-1.0.6 → cytocommunity2-1.0.7}/src/cytocommunity2/__init__.py

@@ -10,7 +10,7 @@ from .learning import (
 )
 from .visualization import visualize_results
 
-__version__ = "1.0.6"
+__version__ = "1.0.7"
 
 __all__ = [
     "CytoCommunityConfig",

{cytocommunity2-1.0.6 → cytocommunity2-1.0.7}/src/cytocommunity2/downstream/plotting/dotplots.py

@@ -10,6 +10,7 @@ from .common import add_colorbar, plotting_style, dot_size, save_figure
 
 
 DOTPLOT_CMAP = "coolwarm"
+DOTPLOT_STRENGTH_VALUES = (0.5, 1.3, 2.0)
 
 
 def _tested_mask(record):
@@ -18,18 +19,8 @@ def _tested_mask(record):
 
 def _panel_size(record):
     tested = _tested_mask(record)
-    return (max(6.0, 0.60 * tested.any(axis=1).sum() + 1.8),
-            max(3.0, 0.60 * tested.any(axis=0).sum() + 1.8))
-
-
-def _legend_strength_values(records):
-    """Choose up to three size examples from the dots actually being drawn."""
-    pvalues = np.concatenate([record["pvalues"][_tested_mask(record)] for record in records])
-    values = np.unique(np.minimum(-np.log10(np.clip(pvalues, 1e-300, 1.0)), 5.0))
-    values[values == 0] = 0.0
-    if len(values) <= 3:
-        return values
-    return values[np.rint(np.linspace(0, len(values) - 1, 3)).astype(int)]
+    return (max(5.4, 0.46 * tested.any(axis=1).sum() + 1.6),
+            max(3.0, 0.46 * tested.any(axis=0).sum() + 1.8))
 
 
 def _draw_panel(
@@ -64,11 +55,11 @@ def _draw_panel(
             x_grid[significant], y_grid[significant], s=60.0, marker="*",
             c="#1d2630", edgecolors="none", zorder=4,
         )
-    axis.set_title(title, fontsize=15, fontweight="bold", pad=10)
+    axis.set_title(title, fontsize=17, fontweight="bold", pad=10)
     axis.set_xticks(np.arange(len(celltypes)))
-    axis.set_xticklabels(celltypes, rotation=rotation, ha="right" if rotation != 90 else "center", fontsize=12)
+    axis.set_xticklabels(celltypes, rotation=rotation, ha="right" if rotation != 90 else "center", fontsize=14)
     axis.set_yticks(np.arange(len(cn_order)))
-    axis.set_yticklabels([f"CN{cn}" for cn in cn_order], fontsize=12)
+    axis.set_yticklabels([f"CN{cn}" for cn in cn_order], fontsize=14)
     axis.set_xlim(-0.6, len(celltypes) - 0.4)
     axis.set_ylim(-0.55, len(cn_order) - 0.45)
     axis.set_aspect("equal", adjustable="box")
@@ -91,20 +82,20 @@ def _draw_dotplot_legend(figure, norm, threshold, colorbar_title,
 
     axis = add_axis([0.04, 0.34, 0.92, 0.64] if compact else [0.04, 0.30, 0.92, 0.65])
     axis.axis("off")
-    values = (1.3, 2.0, 3.0) if strength_values is None else strength_values
+    values = DOTPLOT_STRENGTH_VALUES if strength_values is None else strength_values
     handles = [axis.scatter([], [], s=dot_size(10.0 ** -value), color="#b9414b") for value in values]
     handles.append(axis.scatter([], [], s=60.0, marker="*", color="#1d2630"))
     axis.legend(
         handles, [f"{value:.3g}" for value in values] + [f"p-value < {threshold:g}"],
         title=significance_title, frameon=False, loc="upper left",
         bbox_to_anchor=(0.02, 1.0), labelspacing=0.8 if compact else 1.9, handletextpad=0.75,
-        fontsize=14, title_fontsize=14, markerscale=1.0,
+        fontsize=16, title_fontsize=16, markerscale=1.0,
     )
     colorbar = add_colorbar(figure, add_axis([0.04, 0.06, 0.92, 0.08]), norm,
                             colorbar_title, cmap=DOTPLOT_CMAP, orientation="horizontal")
-    colorbar.ax.tick_params(labelsize=12, pad=3)
+    colorbar.ax.tick_params(labelsize=14, pad=3)
     colorbar.ax.xaxis.set_label_position("top")
-    colorbar.set_label(colorbar_title, fontsize=14, labelpad=6)
+    colorbar.set_label(colorbar_title, fontsize=16, labelpad=6)
 
 
 @plotting_style()
@@ -114,7 +105,7 @@ def save_dotplot_legend(norm, output_dir, threshold=0.05, colorbar_title="log2FC
     """Save a standalone legend for callers that explicitly request one."""
     import matplotlib.pyplot as plt
 
-    figure = plt.figure(figsize=(3.6, 2.55 if compact else 4.15))
+    figure = plt.figure(figsize=(3.6, 3.1 if compact else 4.15))
     _draw_dotplot_legend(figure, norm, threshold, colorbar_title,
                           significance_title, compact=compact, strength_values=strength_values)
     output = save_figure(figure, Path(output_dir) / "LEGEND.pdf", png=png)
@@ -164,7 +155,7 @@ def _save_dotplots(
 
     import matplotlib.pyplot as plt
 
-    strength_values = _legend_strength_values(records)
+    strength_values = DOTPLOT_STRENGTH_VALUES
     outputs = []
     for index, record in enumerate(records):
         figure, axis = plt.subplots(figsize=_panel_size(record))
@@ -199,7 +190,7 @@ def _save_dotplots(
         figure.subplots_adjust(left=0.07 * plot_width / figure_width,
                                right=0.98 * plot_width / figure_width,
                                bottom=0.10, top=0.96, hspace=0.60, wspace=0.25)
-        legend_height = 2.55 if compact_legend else 4.15
+        legend_height = 3.1 if compact_legend else 4.15
         legend_center = 0.96 - 0.86 / rows / 2
         _draw_dotplot_legend(
             figure, norm, threshold, colorbar_title, significance_title,

{cytocommunity2-1.0.6 → cytocommunity2-1.0.7/src/cytocommunity2.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cytocommunity2
-Version: 1.0.6
+Version: 1.0.7
 Summary: Weakly supervised cellular-neighborhood learning for spatial omics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown