Add delta text to forest plot

Author: JAnns98

dabest/forest_plot.py

@@ -10,7 +10,7 @@
 # %matplotlib inline
 import seaborn as sns
 from typing import List, Optional, Union
-
+import numpy as np
 
 # %% ../nbs/API/forest_plot.ipynb 6
 def load_plot_data(
@@ -265,6 +265,7 @@ def get_kwargs(
         horizontal,
         marker_kwargs,
         errorbar_kwargs,
+        delta_text_kwargs,
         marker_size
     ):
     from .misc_tools import merge_two_dicts
@@ -317,7 +318,25 @@ def get_kwargs(
     else:
         errorbar_kwargs = merge_two_dicts(default_errorbar_kwargs, errorbar_kwargs)
 
-    return violin_kwargs, zeroline_kwargs, marker_kwargs, errorbar_kwargs
+
+    # Delta text kwargs
+    default_delta_text_kwargs = {
+                "color": None, 
+                "alpha": 1,
+                "fontsize": 10, 
+                "ha": 'center', 
+                "va": 'center', 
+                "rotation": 0, 
+                "x_coordinates": None, 
+                "y_coordinates": None,
+                "offset": 0
+    }
+    if delta_text_kwargs is None:
+        delta_text_kwargs = default_delta_text_kwargs
+    else:
+        delta_text_kwargs = merge_two_dicts(default_delta_text_kwargs, delta_text_kwargs)
+
+    return violin_kwargs, zeroline_kwargs, marker_kwargs, errorbar_kwargs, delta_text_kwargs
 
 
 def color_palette(
@@ -371,6 +390,9 @@ def forest_plot(
     yticklabels: Optional[list[str]] = None,
     remove_spines: bool = True,
 
+    delta_text: bool = True,
+    delta_text_kwargs: dict = None,
+
     violin_kwargs: Optional[dict] = None,
     zeroline_kwargs: Optional[dict] = None,
     marker_kwargs: Optional[dict] = None,
@@ -426,6 +448,9 @@ def forest_plot(
         Custom y-tick labels for the plot.
     remove_spines : bool, default=True
         If True, removes plot spines (except the relevant dependent variable spine).
+
+
+
     violin_kwargs : Optional[dict], default=None
         Additional arguments for violin plot customization.
     zeroline_kwargs : Optional[dict], default=None
@@ -487,13 +512,15 @@ def forest_plot(
         fig, ax = plt.subplots(figsize=fig_size)
 
     # Get Kwargs
-    violin_kwargs, zeroline_kwargs, marker_kwargs, errorbar_kwargs = get_kwargs(
-                                                                                violin_kwargs = violin_kwargs,
-                                                                                zeroline_kwargs = zeroline_kwargs,
-                                                                                horizontal = horizontal,
-                                                                                marker_kwargs = marker_kwargs,
-                                                                                errorbar_kwargs = errorbar_kwargs,
-                                                                                marker_size = marker_size
+    (violin_kwargs, zeroline_kwargs, 
+    marker_kwargs, errorbar_kwargs, delta_text_kwargs) = get_kwargs(
+                                                            violin_kwargs = violin_kwargs,
+                                                            zeroline_kwargs = zeroline_kwargs,
+                                                            horizontal = horizontal,
+                                                            marker_kwargs = marker_kwargs,
+                                                            errorbar_kwargs = errorbar_kwargs,
+                                                            delta_text_kwargs = delta_text_kwargs,
+                                                            marker_size = marker_size
     )
 
     # Plot the violins and make adjustments
@@ -592,6 +619,48 @@ def forest_plot(
         spines = ["top", "right", "left"] if horizontal else ["top", "right", "bottom"]
         ax.spines[spines].set_visible(False)
 
+    # Delta Text
+    if delta_text:
+        if delta_text_kwargs.get('color') is not None:
+            delta_text_colors = [delta_text_kwargs.pop('color')] * number_of_curves_to_plot
+        else:
+            delta_text_colors = violin_colors
+            delta_text_kwargs.pop('color')
+
+        # Collect the X-coordinates for the delta text
+        delta_text_x_coordinates = delta_text_kwargs.pop('x_coordinates')
+        delta_text_x_adjustment = delta_text_kwargs.pop('offset')
+
+        if delta_text_x_coordinates is not None:
+            if not isinstance(delta_text_x_coordinates, (list, tuple)) or not all(isinstance(x, (int, float)) for x in delta_text_x_coordinates):
+                raise TypeError("delta_text_kwargs['x_coordinates'] must be a list of x-coordinates.")
+            if len(delta_text_x_coordinates) != number_of_curves_to_plot:
+                raise ValueError("delta_text_kwargs['x_coordinates'] must have the same length as the number of ticks to plot.")
+        else:
+            delta_text_x_coordinates = (np.arange(1, number_of_curves_to_plot + 1) 
+                                        + (0.5 if not horizontal else -0.4)
+                                        + delta_text_x_adjustment
+                                    )
+
+        # Collect the Y-coordinates for the delta text
+        delta_text_y_coordinates = delta_text_kwargs.pop('y_coordinates')
+
+        if delta_text_y_coordinates is not None:
+            if not isinstance(delta_text_y_coordinates, (list, tuple)) or not all(isinstance(y, (int, float)) for y in delta_text_y_coordinates):
+                raise TypeError("delta_text_kwargs['y_coordinates'] must be a list of y-coordinates.")
+            if len(delta_text_y_coordinates) != number_of_curves_to_plot:
+                raise ValueError("delta_text_kwargs['y_coordinates'] must have the same length as the number of ticks to plot.")
+        else:
+            delta_text_y_coordinates = differences
+
+        if horizontal:
+            delta_text_x_coordinates, delta_text_y_coordinates = delta_text_y_coordinates, delta_text_x_coordinates
+
+        for idx, x, y, delta in zip(np.arange(0, number_of_curves_to_plot, 1), delta_text_x_coordinates, 
+                                    delta_text_y_coordinates, differences):
+            delta_text = np.format_float_positional(delta, precision=2, sign=True, trim="k", min_digits=2)
+            ax.text(x, y, delta_text, color=delta_text_colors[idx], zorder=5, **delta_text_kwargs)
+
     ## Invert Y-axis if horizontal 
     if horizontal:
         ax.invert_yaxis()

dabest/plot_tools.py

@@ -1164,13 +1164,13 @@ def delta_text_plotter(
 
     # Plot the delta text
     for x,y,t,tick in zip(delta_text_x_coordinates, delta_text_y_coordinates,Delta_Values,ticks_to_plot):
-        Delta_Text = np.format_float_positional(t, precision=2, sign=True, trim="k", min_digits=2)
+        delta_text = np.format_float_positional(t, precision=2, sign=True, trim="k", min_digits=2)
         idx_selector = (
             int(tick)
             if type(delta_text_colors) == list 
             else unpacked_idx[int(tick)]
             )
-        ax_to_plot.text(x, y, Delta_Text, color=delta_text_colors[idx_selector], zorder=5, **delta_text_kwargs)
+        ax_to_plot.text(x, y, delta_text, color=delta_text_colors[idx_selector], zorder=5, **delta_text_kwargs)
 
 
 def delta_dots_plotter(

nbs/API/forest_plot.ipynb

@@ -62,7 +62,8 @@
     "import matplotlib.pyplot as plt\n",
     "# %matplotlib inline\n",
     "import seaborn as sns\n",
-    "from typing import List, Optional, Union\n"
+    "from typing import List, Optional, Union\n",
+    "import numpy as np"
    ]
   },
   {
@@ -324,6 +325,7 @@
     "        horizontal,\n",
     "        marker_kwargs,\n",
     "        errorbar_kwargs,\n",
+    "        delta_text_kwargs,\n",
     "        marker_size\n",
     "    ):\n",
     "    from .misc_tools import merge_two_dicts\n",
@@ -376,7 +378,25 @@
     "    else:\n",
     "        errorbar_kwargs = merge_two_dicts(default_errorbar_kwargs, errorbar_kwargs)\n",
     "\n",
-    "    return violin_kwargs, zeroline_kwargs, marker_kwargs, errorbar_kwargs\n",
+    "\n",
+    "    # Delta text kwargs\n",
+    "    default_delta_text_kwargs = {\n",
+    "                \"color\": None, \n",
+    "                \"alpha\": 1,\n",
+    "                \"fontsize\": 10, \n",
+    "                \"ha\": 'center', \n",
+    "                \"va\": 'center', \n",
+    "                \"rotation\": 0, \n",
+    "                \"x_coordinates\": None, \n",
+    "                \"y_coordinates\": None,\n",
+    "                \"offset\": 0\n",
+    "    }\n",
+    "    if delta_text_kwargs is None:\n",
+    "        delta_text_kwargs = default_delta_text_kwargs\n",
+    "    else:\n",
+    "        delta_text_kwargs = merge_two_dicts(default_delta_text_kwargs, delta_text_kwargs)\n",
+    "\n",
+    "    return violin_kwargs, zeroline_kwargs, marker_kwargs, errorbar_kwargs, delta_text_kwargs\n",
     "\n",
     "\n",
     "def color_palette(\n",
@@ -430,6 +450,9 @@
     "    yticklabels: Optional[list[str]] = None,\n",
     "    remove_spines: bool = True,\n",
     "\n",
+    "    delta_text: bool = True,\n",
+    "    delta_text_kwargs: dict = None,\n",
+    "\n",
     "    violin_kwargs: Optional[dict] = None,\n",
     "    zeroline_kwargs: Optional[dict] = None,\n",
     "    marker_kwargs: Optional[dict] = None,\n",
@@ -485,6 +508,9 @@
     "        Custom y-tick labels for the plot.\n",
     "    remove_spines : bool, default=True\n",
     "        If True, removes plot spines (except the relevant dependent variable spine).\n",
+    "\n",
+    "\n",
+    "\n",
     "    violin_kwargs : Optional[dict], default=None\n",
     "        Additional arguments for violin plot customization.\n",
     "    zeroline_kwargs : Optional[dict], default=None\n",
@@ -546,13 +572,15 @@
     "        fig, ax = plt.subplots(figsize=fig_size)\n",
     "\n",
     "    # Get Kwargs\n",
-    "    violin_kwargs, zeroline_kwargs, marker_kwargs, errorbar_kwargs = get_kwargs(\n",
-    "                                                                                violin_kwargs = violin_kwargs,\n",
-    "                                                                                zeroline_kwargs = zeroline_kwargs,\n",
-    "                                                                                horizontal = horizontal,\n",
-    "                                                                                marker_kwargs = marker_kwargs,\n",
-    "                                                                                errorbar_kwargs = errorbar_kwargs,\n",
-    "                                                                                marker_size = marker_size\n",
+    "    (violin_kwargs, zeroline_kwargs, \n",
+    "    marker_kwargs, errorbar_kwargs, delta_text_kwargs) = get_kwargs(\n",
+    "                                                            violin_kwargs = violin_kwargs,\n",
+    "                                                            zeroline_kwargs = zeroline_kwargs,\n",
+    "                                                            horizontal = horizontal,\n",
+    "                                                            marker_kwargs = marker_kwargs,\n",
+    "                                                            errorbar_kwargs = errorbar_kwargs,\n",
+    "                                                            delta_text_kwargs = delta_text_kwargs,\n",
+    "                                                            marker_size = marker_size\n",
     "    )\n",
     "                                            \n",
     "    # Plot the violins and make adjustments\n",
@@ -651,6 +679,48 @@
     "        spines = [\"top\", \"right\", \"left\"] if horizontal else [\"top\", \"right\", \"bottom\"]\n",
     "        ax.spines[spines].set_visible(False)\n",
     "\n",
+    "    # Delta Text\n",
+    "    if delta_text:\n",
+    "        if delta_text_kwargs.get('color') is not None:\n",
+    "            delta_text_colors = [delta_text_kwargs.pop('color')] * number_of_curves_to_plot\n",
+    "        else:\n",
+    "            delta_text_colors = violin_colors\n",
+    "            delta_text_kwargs.pop('color')\n",
+    "\n",
+    "        # Collect the X-coordinates for the delta text\n",
+    "        delta_text_x_coordinates = delta_text_kwargs.pop('x_coordinates')\n",
+    "        delta_text_x_adjustment = delta_text_kwargs.pop('offset')\n",
+    "\n",
+    "        if delta_text_x_coordinates is not None:\n",
+    "            if not isinstance(delta_text_x_coordinates, (list, tuple)) or not all(isinstance(x, (int, float)) for x in delta_text_x_coordinates):\n",
+    "                raise TypeError(\"delta_text_kwargs['x_coordinates'] must be a list of x-coordinates.\")\n",
+    "            if len(delta_text_x_coordinates) != number_of_curves_to_plot:\n",
+    "                raise ValueError(\"delta_text_kwargs['x_coordinates'] must have the same length as the number of ticks to plot.\")\n",
+    "        else:\n",
+    "            delta_text_x_coordinates = (np.arange(1, number_of_curves_to_plot + 1) \n",
+    "                                        + (0.5 if not horizontal else -0.4)\n",
+    "                                        + delta_text_x_adjustment\n",
+    "                                    )\n",
+    "\n",
+    "        # Collect the Y-coordinates for the delta text\n",
+    "        delta_text_y_coordinates = delta_text_kwargs.pop('y_coordinates')\n",
+    "\n",
+    "        if delta_text_y_coordinates is not None:\n",
+    "            if not isinstance(delta_text_y_coordinates, (list, tuple)) or not all(isinstance(y, (int, float)) for y in delta_text_y_coordinates):\n",
+    "                raise TypeError(\"delta_text_kwargs['y_coordinates'] must be a list of y-coordinates.\")\n",
+    "            if len(delta_text_y_coordinates) != number_of_curves_to_plot:\n",
+    "                raise ValueError(\"delta_text_kwargs['y_coordinates'] must have the same length as the number of ticks to plot.\")\n",
+    "        else:\n",
+    "            delta_text_y_coordinates = differences\n",
+    "\n",
+    "        if horizontal:\n",
+    "            delta_text_x_coordinates, delta_text_y_coordinates = delta_text_y_coordinates, delta_text_x_coordinates\n",
+    "\n",
+    "        for idx, x, y, delta in zip(np.arange(0, number_of_curves_to_plot, 1), delta_text_x_coordinates, \n",
+    "                                    delta_text_y_coordinates, differences):\n",
+    "            delta_text = np.format_float_positional(delta, precision=2, sign=True, trim=\"k\", min_digits=2)\n",
+    "            ax.text(x, y, delta_text, color=delta_text_colors[idx], zorder=5, **delta_text_kwargs)\n",
+    "\n",
     "    ## Invert Y-axis if horizontal \n",
     "    if horizontal:\n",
     "        ax.invert_yaxis()\n",

nbs/API/plot_tools.ipynb

@@ -1214,13 +1214,13 @@
     "\n",
     "    # Plot the delta text\n",
     "    for x,y,t,tick in zip(delta_text_x_coordinates, delta_text_y_coordinates,Delta_Values,ticks_to_plot):\n",
-    "        Delta_Text = np.format_float_positional(t, precision=2, sign=True, trim=\"k\", min_digits=2)\n",
+    "        delta_text = np.format_float_positional(t, precision=2, sign=True, trim=\"k\", min_digits=2)\n",
     "        idx_selector = (\n",
     "            int(tick)\n",
     "            if type(delta_text_colors) == list \n",
     "            else unpacked_idx[int(tick)]\n",
     "            )\n",
-    "        ax_to_plot.text(x, y, Delta_Text, color=delta_text_colors[idx_selector], zorder=5, **delta_text_kwargs)\n",
+    "        ax_to_plot.text(x, y, delta_text, color=delta_text_colors[idx_selector], zorder=5, **delta_text_kwargs)\n",
     "\n",
     "\n",
     "def delta_dots_plotter(\n",

nbs/tests/mpl_image_tests/baseline_images/test_500_deltadelta_forest.png

@@ -390,3 +390,15 @@ def test_519_minimeta_with_deltas_forest():
                 idx=[(0, 3),(0, 3),(0, 3)],
                 labels=['Contrast A1', 'Mini_Meta A', 'Contrast B1', 'Mini_Meta B', 'Contrast C1', 'Mini_Meta C']
             )
+
+@pytest.mark.mpl_image_compare(tolerance=8)
+def test_520_minimeta_with_deltas_and_delta_text_kwargs_forest():
+    plt.rcdefaults()
+    return forest_plot(
+                contrasts_mini_meta, 
+                idx=[(0, 3),(0, 3),(0, 3)],
+                labels=['Contrast A1', 'Mini_Meta A', 'Contrast B1', 'Mini_Meta B', 'Contrast C1', 'Mini_Meta C'],
+                delta_text_kwargs={'color': 'black','fontsize': 8, 'rotation': 45, 'va': 'bottom',
+                                   'x_coordinates': [1.4, 2.4, 3.4, 4.4, 5.4, 6.4], 
+                                   'y_coordinates': [0.6, 0.1, -2, -1.5, -1.5, -1.5]}
+            )

nbs/tests/mpl_image_tests/baseline_images/test_501_deltadelta_with_deltas_idx_forest.png

@@ -1430,7 +1430,7 @@
    "source": [
     "Delta text kwargs can be utilised via `delta_text_kwargs` in the `plot()` function.\n",
     "\n",
-    "The relevant inputs to `summary_bars_kwargs` are:\n",
+    "The relevant inputs to `delta_text_kwargs` are:\n",
     "\n",
     "- `'color'` - Color. If color is not specified, the color of the effect size curve will be used. \n",
     "- `'alpha'`- Alpha (transparency)\n",