Fixes to delta-delta spine in paired condition and added tutorial info for gridkey

Author: JAnns98

dabest/misc_tools.py

@@ -920,8 +920,6 @@ def extract_contrast_plotting_ticks(is_paired, show_pairs, two_col_sankey, plot_
             ticks_to_start_twocol_sankey.pop()
             ticks_to_start_twocol_sankey.insert(0, 0)
         else:
-            # ticks_to_skip = np.arange(0, len(temp_all_plot_groups), 2).tolist()
-            # ticks_to_plot = np.arange(1, len(temp_all_plot_groups), 2).tolist()
             ticks_to_skip = np.cumsum([len(t) for t in idx])[:-1].tolist()
             ticks_to_skip.insert(0, 0)
             # Then obtain the ticks where we have to plot the effect sizes.
@@ -1004,7 +1002,7 @@ def set_xaxis_ticks_and_lims(show_delta2, show_mini_meta, rawdata_axes, contrast
             contrast_axes.set_ylim(rawdata_axes.get_ylim())
         else:
             contrast_axes.set_ylim(rawdata_axes.get_ylim())
-
+    # Vertical
     else:
         # Ticks
         if show_delta2 is False and show_mini_meta is False:
@@ -1025,7 +1023,7 @@ def set_xaxis_ticks_and_lims(show_delta2, show_mini_meta, rawdata_axes, contrast
             # Increase the xlim of raw data by 2
             temp = rawdata_axes.get_xlim()
             if show_pairs:
-                rawdata_axes.set_xlim(temp[0], temp[1] + 0.25)
+                rawdata_axes.set_xlim(temp[0], temp[1] + 0.5)
             else:
                 rawdata_axes.set_xlim(temp[0], temp[1] + 2)
             contrast_axes.set_xlim(rawdata_axes.get_xlim())
@@ -1451,7 +1449,8 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
             rawdata_axes.set_ylim(swarm_ylim[0]-0.5, swarm_ylim[1])
             contrast_axes.set_ylim(contrast_ylim[0]-0.5, contrast_ylim[1])
 
-def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contrast, horizontal):
+def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contrast, horizontal,
+                  show_delta2, delta2_axes):
     """
     Aesthetic general adjustments across both GA and Cumming plots.
 
@@ -1469,6 +1468,10 @@ def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contras
         A boolean flag to determine if the plot is GA or Cum
     horizontal : bool
         A boolean flag to determine if the plot is for horizontal plotting.
+    show_delta2 : bool
+        A boolean flag to determine if the plot will have a delta-delta effect size.
+    delta2_axes : object (Axes)
+        The delta2 axes.
     """
 
     # Because we turned the axes frame off, we also need to draw back the x-spine for both axes.
@@ -1505,11 +1508,22 @@ def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contras
             og_ylim_contrast[1], 
             **redraw_axes_kwargs
         )
+
+        if show_delta2:
+            og_xlim_delta, og_ylim_delta = contrast_axes.get_xlim(), contrast_axes.get_ylim()
+            delta2_axes.set_ylim(og_ylim_delta)
+
+            delta2_axes.vlines(
+                og_xlim_delta[1], 
+                og_ylim_delta[0], 
+                og_ylim_delta[1], 
+                **redraw_axes_kwargs
+            )
+
     for ax, xlim, ylim in zip([rawdata_axes, contrast_axes], [og_xlim_raw, og_xlim_contrast], [og_ylim_raw, og_ylim_contrast]):
         ax.set_xlim(xlim)
         ax.set_ylim(ylim)
 
-    
 def extract_group_summaries(proportional, err_color, rawdata_axes, asymmetric_side, horizontal, 
                             bootstraps_color_by_group, plot_palette_raw, all_plot_groups,
                             n_groups, color_col, ytick_color, plot_kwargs):

dabest/plot_tools.py

@@ -1371,7 +1371,7 @@ def slopegraph_plotter(dabest_obj, plot_data, xvar, yvar, color_col, plot_palett
 def plot_minimeta_or_deltadelta_violins(show_mini_meta, effectsize_df, ci_type, rawdata_axes,
                                         contrast_axes, violinplot_kwargs, halfviolin_alpha, ytick_color, 
                                         es_marker_size, group_summary_kwargs, contrast_xtick_labels, effect_size,
-                                        show_delta2, plot_kwargs, redraw_axes_kwargs, horizontal):
+                                        show_delta2, plot_kwargs, horizontal):
     """
     Add mini meta-analysis or delta-delta violin plots to the contrast plot.
 
@@ -1405,8 +1405,6 @@ def plot_minimeta_or_deltadelta_violins(show_mini_meta, effectsize_df, ci_type,
         Whether to show the delta-delta.
     plot_kwargs : dict
         Keyword arguments for the plot.
-    redraw_axes_kwargs : dict
-        Keyword arguments for the redraw axes.
     horizontal : bool
         If the plot is horizontal.
     """
@@ -1486,7 +1484,7 @@ def plot_minimeta_or_deltadelta_violins(show_mini_meta, effectsize_df, ci_type,
         else:
             contrast_xtick_labels.extend(["", "delta-delta"])
 
-    # Create delta2 axis and label.
+    # Create the delta-delta axes.
     if show_delta2 and not horizontal:
         if plot_kwargs["delta2_label"] is not None:
             delta2_label = plot_kwargs["delta2_label"]
@@ -1500,15 +1498,10 @@ def plot_minimeta_or_deltadelta_violins(show_mini_meta, effectsize_df, ci_type,
         delta2_axes.set_ylabel(delta2_label, fontsize=fontsize_delta2label)
         og_xlim_delta, og_ylim_delta = contrast_axes.get_xlim(), contrast_axes.get_ylim()
         delta2_axes.set_ylim(og_ylim_delta)
-        delta2_axes.vlines(
-            og_xlim_delta[1], 
-            og_ylim_delta[0], 
-            og_ylim_delta[1], 
-            **redraw_axes_kwargs
-        )
-        contrast_axes.set_xlim(og_xlim_delta)
-    
-    return contrast_xtick_labels
+    else:
+        delta2_axes = None
+
+    return delta2_axes, contrast_xtick_labels
 
 
 def effect_size_curve_plotter(ticks_to_plot, results, ci_type, contrast_axes, violinplot_kwargs, halfviolin_alpha, 
@@ -1608,11 +1601,56 @@ def effect_size_curve_plotter(ticks_to_plot, results, ci_type, contrast_axes, vi
         )
     return current_group, current_control, current_effsize, contrast_xtick_labels
 
-
 def gridkey_plotter(is_paired, idx, all_plot_groups, gridkey_rows, rawdata_axes, contrast_axes, 
                  plot_data, xvar, yvar, results, show_delta2, show_mini_meta, 
                  plot_kwargs, x1_level, experiment_label, float_contrast, horizontal,
                  delta_delta, mini_meta_delta, effect_size):
+    """
+    Add gridkey to the contrast plot.
+
+    Parameters
+    ----------
+    is_paired : bool
+        Whether the data is paired.
+    idx : list
+        List of indices of the contrast objects.
+    all_plot_groups : list
+        List of all plot groups.
+    gridkey_rows : list
+        List of gridkey rows.
+    rawdata_axes : object
+        Matplotlib axis object for the raw data.
+    contrast_axes : object
+        Matplotlib axis object for the contrast data.
+    plot_data : object (Dataframe)
+        Dataframe of the plot data.
+    xvar : str
+        Column name of the x variable.
+    yvar : str
+        Column name of the y variable.
+    results : object (Dataframe)
+        Dataframe of contrast object comparisons.
+    show_delta2 : bool
+        Whether to show the delta-delta.
+    show_mini_meta : bool
+        Whether to show the mini meta-analysis.
+    plot_kwargs : dict
+        Keyword arguments for the plot.
+    x1_level : list
+        List of x1 levels.
+    experiment_label : list
+        List of experiment labels.
+    float_contrast : bool
+        Whether the DABEST plot uses Gardner-Altman or Cummings
+    horizontal : bool
+        If the plot is horizontal.
+    delta_delta : object
+        delta-delta object.
+    mini_meta_delta : object
+        Mini meta-analysis object.
+    effect_size : str
+        Type of effect size to plot
+    """
 
     gridkey_delimiters=plot_kwargs["gridkey_delimiters"] # Auto parser for gridkey - implemented by SangyuXu
     if gridkey_rows == "auto":

dabest/plotter.py

@@ -140,8 +140,8 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
     )
 
     # Extract Color palette
-    (color_col, bootstraps_color_by_group, n_groups, filled,
-     swarm_colors, plot_palette_raw, bar_color, 
+    (color_col, bootstraps_color_by_group, n_groups, 
+     filled, swarm_colors, plot_palette_raw, bar_color, 
      plot_palette_bar, plot_palette_contrast, plot_palette_sankey) = get_color_palette(
                                                                                 plot_kwargs=plot_kwargs, 
                                                                                 plot_data=plot_data, 
@@ -359,8 +359,9 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
                                                                     )
 
     # Plot mini-meta or delta-delta violin
+    delta2_axes = None
     if show_mini_meta or show_delta2:
-        contrast_xtick_labels = plot_minimeta_or_deltadelta_violins(
+        delta2_axes, contrast_xtick_labels = plot_minimeta_or_deltadelta_violins(
                                                                 show_mini_meta=show_mini_meta, 
                                                                 effectsize_df=effectsize_df, 
                                                                 ci_type=ci_type, 
@@ -373,9 +374,8 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
                                                                 group_summary_kwargs=group_summary_kwargs, 
                                                                 contrast_xtick_labels=contrast_xtick_labels, 
                                                                 effect_size=effect_size,
-                                                                show_delta2=show_delta2,
-                                                                plot_kwargs=plot_kwargs,
-                                                                redraw_axes_kwargs=redraw_axes_kwargs,
+                                                                show_delta2=show_delta2, 
+                                                                plot_kwargs=plot_kwargs, 
                                                                 horizontal=horizontal,
                                                                 )
 
@@ -433,7 +433,6 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
                                             )
     else:
         # For Cumming Plots only.
-        # skip_redraw_lines = True if plot_kwargs["gridkey_rows"] is not None and not any([show_mini_meta, show_delta2]) else False
         skip_redraw_lines = True if plot_kwargs["gridkey_rows"] is not None else False
         Cumming_Plot_Aesthetic_Adjustments(
                                     contrast_axes=contrast_axes, 
@@ -461,7 +460,9 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
         contrast_axes=contrast_axes, 
         redraw_axes_kwargs=redraw_axes_kwargs, 
         float_contrast=float_contrast, 
-        horizontal=horizontal
+        horizontal=horizontal,
+        show_delta2=show_delta2, 
+        delta2_axes=delta2_axes
         )
 
     # Swarm bars WIP
@@ -503,80 +504,77 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
     summary_bars = plot_kwargs["summary_bars"]
     if summary_bars is not None and not horizontal:
         summary_bars_plotter(
-                        summary_bars=summary_bars, 
-                        results=results, 
-                        ax_to_plot=contrast_axes, 
-                        float_contrast=float_contrast,
-                        summary_bars_kwargs=summary_bars_kwargs, 
-                        ci_type=ci_type, 
-                        ticks_to_plot=ticks_to_plot, 
-                        color_col=color_col,
-                        plot_palette_raw=plot_palette_raw, 
-                        proportional=proportional, 
-                        is_paired=is_paired
+                        summary_bars = summary_bars, 
+                        results = results, 
+                        ax_to_plot = contrast_axes, 
+                        float_contrast = float_contrast,
+                        summary_bars_kwargs = summary_bars_kwargs, 
+                        ci_type = ci_type, 
+                        ticks_to_plot = ticks_to_plot, 
+                        color_col = color_col,
+                        plot_palette_raw = plot_palette_raw, 
+                        proportional = proportional, 
+                        is_paired = is_paired
                         )
     # Delta text WIP
     delta_text = plot_kwargs["delta_text"]
     if delta_text and not horizontal: 
         delta_text_plotter(
-                    results=results, 
-                    ax_to_plot=contrast_axes, 
-                    swarm_plot_ax=rawdata_axes, 
-                    ticks_to_plot=ticks_to_plot, 
-                    delta_text_kwargs=delta_text_kwargs, 
-                    color_col=color_col, 
-                    plot_palette_raw=plot_palette_raw, 
-                    is_paired=is_paired,
-                    proportional=proportional, 
-                    float_contrast=float_contrast, 
-                    show_mini_meta=show_mini_meta, 
-                    mini_meta_delta=effectsize_df.mini_meta_delta if show_mini_meta else None, 
-                    show_delta2=show_delta2, 
-                    delta_delta=effectsize_df.delta_delta if show_delta2 else None,
-                    idx=idx
+                    results = results, 
+                    ax_to_plot = contrast_axes, 
+                    swarm_plot_ax = rawdata_axes, 
+                    ticks_to_plot = ticks_to_plot, 
+                    delta_text_kwargs = delta_text_kwargs, 
+                    color_col = color_col, 
+                    plot_palette_raw = plot_palette_raw, 
+                    is_paired = is_paired,
+                    proportional = proportional, 
+                    float_contrast = float_contrast, 
+                    show_mini_meta = show_mini_meta, 
+                    mini_meta_delta = effectsize_df.mini_meta_delta if show_mini_meta else None, 
+                    show_delta2 = show_delta2, 
+                    delta_delta = effectsize_df.delta_delta if show_delta2 else None,
+                    idx = idx
                     )
 
     # Table Axes for horizontal plots
     if horizontal:
         table_for_horizontal_plots(
-                            effectsize_df=effectsize_df,
+                            effectsize_df = effectsize_df,
                             ax = table_axes,
-                            contrast_axes=contrast_axes,
-                            ticks_to_plot=table_axes_ticks_to_plot, 
-                            show_mini_meta=show_mini_meta,
-                            show_delta2=show_delta2,
-                            table_kwargs=table_kwargs,
+                            contrast_axes = contrast_axes,
+                            ticks_to_plot = table_axes_ticks_to_plot, 
+                            show_mini_meta = show_mini_meta,
+                            show_delta2 = show_delta2,
+                            table_kwargs = table_kwargs,
                             )
-        
 
-    # GRIDKEY  WIP
+    # GRIDKEY
     gridkey_rows = plot_kwargs["gridkey_rows"]
-    # if gridkey_rows is not None and not any([show_mini_meta, show_delta2]):
     if gridkey_rows is not None:
         gridkey_plotter(
-                is_paired=is_paired, 
-                idx=idx, 
-                all_plot_groups=all_plot_groups, 
-                gridkey_rows=gridkey_rows, 
+                is_paired = is_paired, 
+                idx = idx, 
+                all_plot_groups = all_plot_groups, 
+                gridkey_rows = gridkey_rows, 
                 rawdata_axes = rawdata_axes,
                 contrast_axes = contrast_axes,
-                plot_data=plot_data, 
-                xvar=xvar, 
-                yvar=yvar, 
-                results=results, 
-                show_delta2=show_delta2, 
-                show_mini_meta=show_mini_meta, 
-                plot_kwargs=plot_kwargs,
-                x1_level=x1_level,
-                experiment_label=experiment_label,
-                float_contrast=float_contrast,
-                horizontal=horizontal,
+                plot_data = plot_data, 
+                xvar = xvar, 
+                yvar = yvar, 
+                results = results, 
+                show_delta2 = show_delta2, 
+                show_mini_meta = show_mini_meta, 
+                plot_kwargs = plot_kwargs,
+                x1_level = x1_level,
+                experiment_label = experiment_label,
+                float_contrast = float_contrast,
+                horizontal = horizontal,
                 delta_delta = effectsize_df.delta_delta if show_delta2 else None,
                 mini_meta_delta = effectsize_df.mini_meta_delta if show_mini_meta else None,
                 effect_size = effect_size,
                 )
 
-
     # Make sure no stray ticks appear!
     rawdata_axes.xaxis.set_ticks_position("bottom")
     rawdata_axes.yaxis.set_ticks_position("left")