Adjusted alpha values for swarm and contrast bars

Author: JAnns98

dabest/_effsize_objects.py

@@ -1196,11 +1196,11 @@ def plot(
         contrast_bars_kwargs : dict, default None
             Pass relevant keyword arguments to the contrast bars. Pass any keyword arguments accepted by 
             matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:
-            {"color": None, "alpha": 0.3, "zorder":-3}
+            {"color": None, "zorder":-3}
         swarm_bars_kwargs : dict, default None
             Pass relevant keyword arguments to the swarm bars. Pass any keyword arguments accepted by 
             matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:
-            {"color": None, "alpha": 0.3, "zorder":-3}
+            {"color": None, "zorder":-3}
 
         summary_bars : list, default None
             Pass a list of indices of the contrast objects to have summary bars displayed on the plot.

dabest/misc_tools.py

@@ -362,7 +362,6 @@ def get_kwargs(plot_kwargs, ytick_color):
     # Swarm bars kwargs.
     default_swarm_bars_kwargs = {
                     "color": None, 
-                    "alpha": 0.3,
                     "zorder":-3
     }
     if plot_kwargs["swarm_bars_kwargs"] is None:
@@ -373,7 +372,6 @@ def get_kwargs(plot_kwargs, ytick_color):
     # Contrast bars kwargs.
     default_contrast_bars_kwargs = {
                     "color": None, 
-                    "alpha": 0.3,
                     "zorder":-3
     }
     if plot_kwargs["contrast_bars_kwargs"] is None:

dabest/plot_tools.py

@@ -1007,6 +1007,7 @@ def contrast_bars_plotter(results: object, ax_to_plot: object,  swarm_plot_ax: o
 
     unpacked_idx = [element for innerList in idx for element in innerList] 
 
+    # Colors
     contrast_bars_colors = (
         [contrast_bars_kwargs.get('color')] * int(max(ticks_to_plot) + 1) 
         if contrast_bars_kwargs.get('color') is not None 
@@ -1016,6 +1017,9 @@ def contrast_bars_plotter(results: object, ax_to_plot: object,  swarm_plot_ax: o
     )
     contrast_bars_kwargs.pop('color')
 
+    # alpha
+    contrast_bars_kwargs['alpha'] = contrast_bars_kwargs.get('alpha', 0.15 if color_col is not None or is_paired else 0.25)
+
     for contrast_bars_x,contrast_bars_y in zip(ticks_to_plot, contrast_means):
         idx_selector = (
             int(contrast_bars_x) 
@@ -1032,7 +1036,7 @@ def contrast_bars_plotter(results: object, ax_to_plot: object,  swarm_plot_ax: o
         if horizontal:
             ax_to_plot.add_patch(mpatches.Rectangle((0, max(swarm_plot_ax.get_yticks())-0.5), diff, 0.5, color='black', **contrast_bars_kwargs))
         else:
-            ax_to_plot.add_patch(mpatches.Rectangle((max(swarm_plot_ax.get_xticks())+2-0.25,0),0.5, diff, color='black', **contrast_bars_kwargs))
+            ax_to_plot.add_patch(mpatches.Rectangle((max(swarm_plot_ax.get_xticks())+2-0.25, 0), 0.5, diff, color='black', **contrast_bars_kwargs))
 
     ax_to_plot.set_xlim(og_xlim)
     ax_to_plot.set_ylim(og_ylim)
@@ -1075,6 +1079,7 @@ def swarm_bars_plotter(plot_data: object, xvar: str, yvar: str, ax: object,
 
     unpacked_idx = [element for innerList in idx for element in innerList] 
 
+    # Colors
     swarm_bars_colors = (
         [swarm_bars_kwargs.get('color')] * (len(swarm_bars_order) + 1) 
         if swarm_bars_kwargs.get('color') is not None 
@@ -1084,6 +1089,9 @@ def swarm_bars_plotter(plot_data: object, xvar: str, yvar: str, ax: object,
         )
     swarm_bars_kwargs.pop('color')
 
+    # alpha
+    swarm_bars_kwargs['alpha'] = swarm_bars_kwargs.get('alpha', 0.15 if color_col is not None or is_paired else 0.25)
+
     for swarm_bars_x,swarm_bars_y in zip(np.arange(0,len(swarm_bars_order)+1,1), swarm_means):
         idx_selector = (
             swarm_bars_x

nbs/API/effsize_objects.ipynb

@@ -1355,11 +1355,11 @@
     "        contrast_bars_kwargs : dict, default None\n",
     "            Pass relevant keyword arguments to the contrast bars. Pass any keyword arguments accepted by \n",
     "            matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:\n",
-    "            {\"color\": None, \"alpha\": 0.3, \"zorder\":-3}\n",
+    "            {\"color\": None, \"zorder\":-3}\n",
     "        swarm_bars_kwargs : dict, default None\n",
     "            Pass relevant keyword arguments to the swarm bars. Pass any keyword arguments accepted by \n",
     "            matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:\n",
-    "            {\"color\": None, \"alpha\": 0.3, \"zorder\":-3}\n",
+    "            {\"color\": None, \"zorder\":-3}\n",
     "\n",
     "        summary_bars : list, default None\n",
     "            Pass a list of indices of the contrast objects to have summary bars displayed on the plot.\n",

nbs/API/misc_tools.ipynb

@@ -415,7 +415,6 @@
     "    # Swarm bars kwargs.\n",
     "    default_swarm_bars_kwargs = {\n",
     "                    \"color\": None, \n",
-    "                    \"alpha\": 0.3,\n",
     "                    \"zorder\":-3\n",
     "    }\n",
     "    if plot_kwargs[\"swarm_bars_kwargs\"] is None:\n",
@@ -426,7 +425,6 @@
     "    # Contrast bars kwargs.\n",
     "    default_contrast_bars_kwargs = {\n",
     "                    \"color\": None, \n",
-    "                    \"alpha\": 0.3,\n",
     "                    \"zorder\":-3\n",
     "    }\n",
     "    if plot_kwargs[\"contrast_bars_kwargs\"] is None:\n",

nbs/API/plot_tools.ipynb

@@ -1057,6 +1057,7 @@
     "\n",
     "    unpacked_idx = [element for innerList in idx for element in innerList] \n",
     "\n",
+    "    # Colors\n",
     "    contrast_bars_colors = (\n",
     "        [contrast_bars_kwargs.get('color')] * int(max(ticks_to_plot) + 1) \n",
     "        if contrast_bars_kwargs.get('color') is not None \n",
@@ -1066,6 +1067,9 @@
     "    )\n",
     "    contrast_bars_kwargs.pop('color')\n",
     "\n",
+    "    # alpha\n",
+    "    contrast_bars_kwargs['alpha'] = contrast_bars_kwargs.get('alpha', 0.15 if color_col is not None or is_paired else 0.25)\n",
+    "\n",
     "    for contrast_bars_x,contrast_bars_y in zip(ticks_to_plot, contrast_means):\n",
     "        idx_selector = (\n",
     "            int(contrast_bars_x) \n",
@@ -1082,7 +1086,7 @@
     "        if horizontal:\n",
     "            ax_to_plot.add_patch(mpatches.Rectangle((0, max(swarm_plot_ax.get_yticks())-0.5), diff, 0.5, color='black', **contrast_bars_kwargs))\n",
     "        else:\n",
-    "            ax_to_plot.add_patch(mpatches.Rectangle((max(swarm_plot_ax.get_xticks())+2-0.25,0),0.5, diff, color='black', **contrast_bars_kwargs))\n",
+    "            ax_to_plot.add_patch(mpatches.Rectangle((max(swarm_plot_ax.get_xticks())+2-0.25, 0), 0.5, diff, color='black', **contrast_bars_kwargs))\n",
     "\n",
     "    ax_to_plot.set_xlim(og_xlim)\n",
     "    ax_to_plot.set_ylim(og_ylim)\n",
@@ -1125,6 +1129,7 @@
     "\n",
     "    unpacked_idx = [element for innerList in idx for element in innerList] \n",
     "\n",
+    "    # Colors\n",
     "    swarm_bars_colors = (\n",
     "        [swarm_bars_kwargs.get('color')] * (len(swarm_bars_order) + 1) \n",
     "        if swarm_bars_kwargs.get('color') is not None \n",
@@ -1134,6 +1139,9 @@
     "        )\n",
     "    swarm_bars_kwargs.pop('color')\n",
     "\n",
+    "    # alpha\n",
+    "    swarm_bars_kwargs['alpha'] = swarm_bars_kwargs.get('alpha', 0.15 if color_col is not None or is_paired else 0.25)\n",
+    "\n",
     "    for swarm_bars_x,swarm_bars_y in zip(np.arange(0,len(swarm_bars_order)+1,1), swarm_means):\n",
     "        idx_selector = (\n",
     "            swarm_bars_x\n",