Add some docstrings and remove a few redundant lines

JAnns98 · JAnns98 · commit 794baedf1f16 · 2025-03-13T16:56:03.000+08:00
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-DABEST-Python
-================
+# DABEST-Python
+
 
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
diff --git a/dabest/misc_tools.py b/dabest/misc_tools.py
@@ -1355,7 +1355,7 @@ def gardner_altman_adjustments(
         redraw_axes_kwargs: dict
     ):
     """
-    Aesthetic adjustments for the Gardner-Altman plot.
+    Aesthetic adjustments specific to Gardner-Altman plots (float_contrast=True).
     
     Parameters
     ----------
@@ -1546,6 +1546,20 @@ def draw_zeroline(
         reflines_kwargs : dict,
         extra_delta : bool,
     ):
+    """
+    Draw the independent axis spine lines.
+
+    Parameters
+    ----------
+    ax : object (Axes)
+        The contrast data axes.
+    horizontal : bool
+        A boolean flag to determine if the plot is for horizontal plotting.
+    reflines_kwargs : dict
+        Additional keyword arguments to be passed to the zeroline.
+    extra_delta : bool
+        A boolean flag to determine if the plot includes an extra delta (delta-delta or mini-meta).
+    """
     # If 0 lies within the ylim of the contrast axes, draw a zero reference line.
     if extra_delta and not horizontal:
         contrast_xlim = [-0.5, 3.4]
@@ -1584,9 +1598,40 @@ def redraw_independent_spines(
         ticks_to_skip : list,
         temp_idx : list,
         ticks_to_skip_contrast : list,
-        extra_delta : bool,
         redraw_axes_kwargs : dict
     ):
+    """
+    Draw the independent axis spine lines.
+
+    Parameters
+    ----------
+    rawdata_axes : object (Axes)
+        The raw data axes.
+    contrast_axes : object (Axes)
+        The contrast axes.
+    horizontal : bool
+        A boolean flag to determine if the plot is for horizontal plotting.
+    two_col_sankey : bool
+        A boolean flag to determine if the plot is for two-col sankey.
+    ticks_to_start_twocol_sankey : list
+        A list of ticks to start for sankey plot.
+    idx : list
+        A list of indices.
+    is_paired : bool
+        A boolean flag to determine if the data is paired.
+    show_pairs : bool
+        A boolean flag to determine if pairs should be shown.
+    proportional : bool
+        A boolean flag to determine if the plot is proportional/binary.
+    ticks_to_skip : list,
+        A list of ticks to be skipped in the raw data axes.
+    temp_idx : list,
+        A temporary list of indices to be used for skipping ticks in the raw data axes.
+    ticks_to_skip_contrast : list,
+        A list of ticks to be skipped in the contrast axes.
+    redraw_axes_kwargs : dict
+        Kwargs passed to the redraw axes.
+    """
     # Extract the ticks
     if two_col_sankey:
         rightend_ticks_raw = rightend_ticks_contrast = np.array([len(i) - 2 for i in idx]) + np.array(ticks_to_start_twocol_sankey)
@@ -1655,7 +1700,7 @@ def redraw_dependent_spines(
         delta2_axes: axes.Axes
     ):
     """
-    Aesthetic general adjustments across both GA and Cumming plots.
+    Draw the dependent axis spine lines.
 
     Parameters
     ----------
@@ -1665,8 +1710,6 @@ def redraw_dependent_spines(
         The contrast axes.
     redraw_axes_kwargs : dict
         Kwargs passed to the redraw axes.
-    plot_kwargs : dict
-        Kwargs passed to the plot function.
     float_contrast : bool
         A boolean flag to determine if the plot is GA or Cum
     horizontal : bool
diff --git a/dabest/plot_tools.py b/dabest/plot_tools.py
@@ -887,7 +887,6 @@ def summary_bars_plotter(
         ticks_to_plot: list, 
         color_col: str, 
         plot_palette_raw: dict, 
-        proportional: bool, 
         show_pairs: bool, 
         horizontal: bool
     ):
@@ -914,8 +913,6 @@ def summary_bars_plotter(
         Column name of the color column.
     plot_palette_raw : dict
         Dictionary of colors used in the plot.
-    proportional : bool
-        Whether the data is proportional.
     show_pairs : bool
         Whether the data is paired and shown in pairs.
     horizontal : bool
@@ -1055,8 +1052,7 @@ def delta_text_plotter(
         delta_text_kwargs: dict, 
         color_col: str, 
         plot_palette_raw: dict, 
-        show_pairs: bool, 
-        proportional: bool, 
+        show_pairs: bool,
         float_contrast: bool,
         show_mini_meta: bool, 
         mini_meta: object, 
@@ -1085,8 +1081,6 @@ def delta_text_plotter(
         Dictionary of colors used in the plot.
     show_pairs : bool
         Whether the data is paired and show pairs.
-    proportional : bool
-        Whether the data is proportional.
     float_contrast : bool
         Whether the DABEST plot uses Gardner-Altman or Cummings
     show_mini_meta : bool
@@ -2055,7 +2049,6 @@ def barplotter(
         raw_colors: str, 
         plot_palette_raw: dict, 
         color_col: str,
-        plot_kwargs: dict, 
         barplot_kwargs: dict, 
         horizontal: bool
     ):
@@ -2080,8 +2073,6 @@ def barplotter(
         Dictionary of colors used in the bar plot.
     color_col : str
         Column name of the color column.
-    plot_kwargs : dict
-        Keyword arguments for the plot.
     barplot_kwargs : dict
         Keyword arguments for the barplot.
     horizontal : bool
@@ -2143,7 +2134,6 @@ def barplotter(
     )
 
     # adjust the width of bars
-    # bar_width = plot_kwargs["bar_width"]
     if horizontal:
         for bar in bar1.patches:
             y = bar.get_y()
diff --git a/dabest/plotter.py b/dabest/plotter.py
@@ -247,7 +247,6 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
                 raw_colors = raw_colors, 
                 plot_palette_raw = plot_palette_raw, 
                 color_col = color_col,
-                plot_kwargs = plot_kwargs, 
                 barplot_kwargs = barplot_kwargs,
                 horizontal = horizontal,
             )
@@ -440,7 +439,6 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
                     color_col = color_col, 
                     plot_palette_raw = plot_palette_raw, 
                     show_pairs = show_pairs,
-                    proportional = proportional, 
                     float_contrast = float_contrast, 
                     show_mini_meta = show_mini_meta, 
                     mini_meta = effectsize_df.mini_meta if show_mini_meta else None, 
@@ -507,7 +505,6 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
                         ticks_to_skip = ticks_to_skip,
                         temp_idx = temp_idx if is_paired == "baseline" and show_pairs else None,
                         ticks_to_skip_contrast = ticks_to_skip_contrast,
-                        extra_delta = True if (show_delta2 or show_mini_meta) else False,
                         redraw_axes_kwargs = redraw_axes_kwargs
             )
 
@@ -587,7 +584,6 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
                         ticks_to_plot = ticks_to_plot, 
                         color_col = color_col,
                         plot_palette_raw = plot_palette_raw, 
-                        proportional = proportional, 
                         show_pairs = show_pairs,
                         horizontal = horizontal,
         )
diff --git a/nbs/API/misc_tools.ipynb b/nbs/API/misc_tools.ipynb
@@ -1409,7 +1409,7 @@
     "        redraw_axes_kwargs: dict\n",
     "    ):\n",
     "    \"\"\"\n",
-    "    Aesthetic adjustments for the Gardner-Altman plot.\n",
+    "    Aesthetic adjustments specific to Gardner-Altman plots (float_contrast=True).\n",
     "    \n",
     "    Parameters\n",
     "    ----------\n",
@@ -1600,6 +1600,20 @@
     "        reflines_kwargs : dict,\n",
     "        extra_delta : bool,\n",
     "    ):\n",
+    "    \"\"\"\n",
+    "    Draw the independent axis spine lines.\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    ax : object (Axes)\n",
+    "        The contrast data axes.\n",
+    "    horizontal : bool\n",
+    "        A boolean flag to determine if the plot is for horizontal plotting.\n",
+    "    reflines_kwargs : dict\n",
+    "        Additional keyword arguments to be passed to the zeroline.\n",
+    "    extra_delta : bool\n",
+    "        A boolean flag to determine if the plot includes an extra delta (delta-delta or mini-meta).\n",
+    "    \"\"\"\n",
     "    # If 0 lies within the ylim of the contrast axes, draw a zero reference line.\n",
     "    if extra_delta and not horizontal:\n",
     "        contrast_xlim = [-0.5, 3.4]\n",
@@ -1638,9 +1652,40 @@
     "        ticks_to_skip : list,\n",
     "        temp_idx : list,\n",
     "        ticks_to_skip_contrast : list,\n",
-    "        extra_delta : bool,\n",
     "        redraw_axes_kwargs : dict\n",
     "    ):\n",
+    "    \"\"\"\n",
+    "    Draw the independent axis spine lines.\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    rawdata_axes : object (Axes)\n",
+    "        The raw data axes.\n",
+    "    contrast_axes : object (Axes)\n",
+    "        The contrast axes.\n",
+    "    horizontal : bool\n",
+    "        A boolean flag to determine if the plot is for horizontal plotting.\n",
+    "    two_col_sankey : bool\n",
+    "        A boolean flag to determine if the plot is for two-col sankey.\n",
+    "    ticks_to_start_twocol_sankey : list\n",
+    "        A list of ticks to start for sankey plot.\n",
+    "    idx : list\n",
+    "        A list of indices.\n",
+    "    is_paired : bool\n",
+    "        A boolean flag to determine if the data is paired.\n",
+    "    show_pairs : bool\n",
+    "        A boolean flag to determine if pairs should be shown.\n",
+    "    proportional : bool\n",
+    "        A boolean flag to determine if the plot is proportional/binary.\n",
+    "    ticks_to_skip : list,\n",
+    "        A list of ticks to be skipped in the raw data axes.\n",
+    "    temp_idx : list,\n",
+    "        A temporary list of indices to be used for skipping ticks in the raw data axes.\n",
+    "    ticks_to_skip_contrast : list,\n",
+    "        A list of ticks to be skipped in the contrast axes.\n",
+    "    redraw_axes_kwargs : dict\n",
+    "        Kwargs passed to the redraw axes.\n",
+    "    \"\"\"\n",
     "    # Extract the ticks\n",
     "    if two_col_sankey:\n",
     "        rightend_ticks_raw = rightend_ticks_contrast = np.array([len(i) - 2 for i in idx]) + np.array(ticks_to_start_twocol_sankey)\n",
@@ -1709,7 +1754,7 @@
     "        delta2_axes: axes.Axes\n",
     "    ):\n",
     "    \"\"\"\n",
-    "    Aesthetic general adjustments across both GA and Cumming plots.\n",
+    "    Draw the dependent axis spine lines.\n",
     "\n",
     "    Parameters\n",
     "    ----------\n",
@@ -1719,8 +1764,6 @@
     "        The contrast axes.\n",
     "    redraw_axes_kwargs : dict\n",
     "        Kwargs passed to the redraw axes.\n",
-    "    plot_kwargs : dict\n",
-    "        Kwargs passed to the plot function.\n",
     "    float_contrast : bool\n",
     "        A boolean flag to determine if the plot is GA or Cum\n",
     "    horizontal : bool\n",
diff --git a/nbs/API/plot_tools.ipynb b/nbs/API/plot_tools.ipynb
@@ -937,7 +937,6 @@
     "        ticks_to_plot: list, \n",
     "        color_col: str, \n",
     "        plot_palette_raw: dict, \n",
-    "        proportional: bool, \n",
     "        show_pairs: bool, \n",
     "        horizontal: bool\n",
     "    ):\n",
@@ -964,8 +963,6 @@
     "        Column name of the color column.\n",
     "    plot_palette_raw : dict\n",
     "        Dictionary of colors used in the plot.\n",
-    "    proportional : bool\n",
-    "        Whether the data is proportional.\n",
     "    show_pairs : bool\n",
     "        Whether the data is paired and shown in pairs.\n",
     "    horizontal : bool\n",
@@ -1105,8 +1102,7 @@
     "        delta_text_kwargs: dict, \n",
     "        color_col: str, \n",
     "        plot_palette_raw: dict, \n",
-    "        show_pairs: bool, \n",
-    "        proportional: bool, \n",
+    "        show_pairs: bool,\n",
     "        float_contrast: bool,\n",
     "        show_mini_meta: bool, \n",
     "        mini_meta: object, \n",
@@ -1135,8 +1131,6 @@
     "        Dictionary of colors used in the plot.\n",
     "    show_pairs : bool\n",
     "        Whether the data is paired and show pairs.\n",
-    "    proportional : bool\n",
-    "        Whether the data is proportional.\n",
     "    float_contrast : bool\n",
     "        Whether the DABEST plot uses Gardner-Altman or Cummings\n",
     "    show_mini_meta : bool\n",
@@ -2105,7 +2099,6 @@
     "        raw_colors: str, \n",
     "        plot_palette_raw: dict, \n",
     "        color_col: str,\n",
-    "        plot_kwargs: dict, \n",
     "        barplot_kwargs: dict, \n",
     "        horizontal: bool\n",
     "    ):\n",
@@ -2130,8 +2123,6 @@
     "        Dictionary of colors used in the bar plot.\n",
     "    color_col : str\n",
     "        Column name of the color column.\n",
-    "    plot_kwargs : dict\n",
-    "        Keyword arguments for the plot.\n",
     "    barplot_kwargs : dict\n",
     "        Keyword arguments for the barplot.\n",
     "    horizontal : bool\n",
@@ -2193,7 +2184,6 @@
     "    )\n",
     "\n",
     "    # adjust the width of bars\n",
-    "    # bar_width = plot_kwargs[\"bar_width\"]\n",
     "    if horizontal:\n",
     "        for bar in bar1.patches:\n",
     "            y = bar.get_y()\n",
diff --git a/nbs/API/plotter.ipynb b/nbs/API/plotter.ipynb
