Added empty_circle plot aesthetic

.gitignore

@@ -5,6 +5,7 @@ _proc/
 .gitattributes
 .last_checked
 .gitconfig
+.cursorignore
 *.bak
 *.log
 *~

dabest/_api.py

@@ -1,3 +1,5 @@
+"""Loading data and relevant groups"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/load.ipynb.
 
 # %% auto 0

dabest/_dabest_object.py

@@ -1,3 +1,5 @@
+"""Main class for estimating statistics and generating plots."""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/dabest_object.ipynb.
 
 # %% auto 0

dabest/_delta_objects.py

@@ -1,3 +1,5 @@
+"""Auxiliary delta classes for estimating statistics and generating plots."""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/delta_objects.ipynb.
 
 # %% auto 0

dabest/_effsize_objects.py

@@ -1,3 +1,5 @@
+"""The auxiliary classes involved in the computations of bootstrapped effect sizes."""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/effsize_objects.ipynb.
 
 # %% auto 0
@@ -971,6 +973,7 @@ def plot(
         contrast_ylim=None,
         delta2_ylim=None,
         swarm_side=None,
+        empty_circle=False,
         custom_palette=None,
         swarm_desat=0.5,
         halfviolin_desat=1,
@@ -994,10 +997,6 @@ def plot(
         fig_size=None,
         dpi=100,
         ax=None,
-        contrast_show_es=False,
-        es_sf=2,
-        es_fontsize=10,
-        contrast_show_deltas=True,
         gridkey_rows=None,
         gridkey_merge_pairs=False,
         gridkey_show_Ns=True,
@@ -1017,6 +1016,17 @@ def plot(
         fontsize_contrastxlabel=12,
         fontsize_contrastylabel=12,
         fontsize_delta2label=12,
+        #### Contrast bars and delta text and delta dots WIP  ####
+        contrast_bars=True,
+        swarm_bars=True,
+        contrast_bars_kwargs=None,
+        swarm_bars_kwargs=None,
+        summary_bars=None,
+        summary_bars_kwargs=None,
+        delta_text=True,
+        delta_text_kwargs=None,
+        delta_dot=True,
+        delta_dot_kwargs=None,
     ):
         """
         Creates an estimation plot for the effect size of interest.
@@ -1064,6 +1074,12 @@ def plot(
             https://seaborn.pydata.org/generated/seaborn.cubehelix_palette.html
             The named colors of matplotlib can be found here:
             https://matplotlib.org/examples/color/named_colors.html
+        swarm_side: string, default None
+            The side on which points are swarmed for swarmplots ("center", "left", or "right").
+        empty_circle: boolean, default False
+            Boolean value determining if empty circles will be used for plotting of
+            swarmplot for control groups. Color of each individual swarm is also now
+            dependent on the comparison group.
         swarm_desat : float, default 1
             Decreases the saturation of the colors in the swarmplot by the
             desired proportion. Uses `seaborn.desaturate()` to acheive this.
@@ -1159,7 +1175,39 @@ def plot(
             Font size for the contrast axes ylabel.
         fontsize_delta2label : float, default 12
             Font size for the delta-delta axes ylabel.
-
+
+
+        contrast_bars : boolean, default True
+            Whether or not to display the contrast bars.
+        swarm_bars : boolean, default True
+            Whether or not to display the swarm bars.
+        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}
+        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}
+
+        summary_bars : list, default None
+            Pass a list of indices of the contrast objects to have summary bars displayed on the plot.
+            For example, [0,1] will show summary bars for the first two contrast objects.
+        summary_bars_kwargs: dict, default None
+            If None, the following keywords are passed: {"color": None, "alpha": 0.15}
+        delta_text : boolean, default True
+            Whether or not to display the text deltas.
+        delta_text_kwargs : dict, default None
+            Pass relevant keyword arguments to the delta text. Pass any keyword arguments accepted by
+            matplotlib.text.Text here, as a string. If None, the following keywords are passed:
+            {"color": None, "alpha": 1, "fontsize": 10, "ha": 'center', "va": 'center', "rotation": 0, 
+            "x_location": 'right', "x_coordinates": None, "y_coordinates": None}
+            Use "x_coordinates" and "y_coordinates" if you would like to specify the text locations manually.
+        delta_dot : boolean, default True
+            Whether or not to display the delta dots on paired or repeated measure plots.
+        delta_dot_kwargs : dict, default None
+            Pass relevant keyword arguments. If None, the following keywords are passed:
+            {"marker": "^", "alpha": 0.5, "zorder": 2, "size": 3, "side": "right"}
 
         Returns
         -------
@@ -1180,7 +1228,7 @@ def plot(
         if hasattr(self, "results") is False:
             self.__pre_calc()
 
-        if self.__delta2:
+        if self.__delta2 and not empty_circle:
             color_col = self.__x2
 
         # if self.__proportional:

dabest/_modidx.py

@@ -65,11 +65,30 @@
                                                                               'dabest/forest_plot.py'),
                                     'dabest.forest_plot.forest_plot': ('API/forest_plot.html#forest_plot', 'dabest/forest_plot.py'),
                                     'dabest.forest_plot.load_plot_data': ('API/forest_plot.html#load_plot_data', 'dabest/forest_plot.py')},
-            'dabest.misc_tools': { 'dabest.misc_tools.get_varname': ('API/misc_tools.html#get_varname', 'dabest/misc_tools.py'),
+            'dabest.misc_tools': { 'dabest.misc_tools.Cumming_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#cumming_plot_aesthetic_adjustments',
+                                                                                             'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.Gardner_Altman_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#gardner_altman_plot_aesthetic_adjustments',
+                                                                                                    'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.General_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#general_plot_aesthetic_adjustments',
+                                                                                             'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.add_counts_to_ticks': ( 'API/misc_tools.html#add_counts_to_ticks',
+                                                                              'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.extract_contrast_plotting_ticks': ( 'API/misc_tools.html#extract_contrast_plotting_ticks',
+                                                                                          'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.get_color_palette': ('API/misc_tools.html#get_color_palette', 'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.get_kwargs': ('API/misc_tools.html#get_kwargs', 'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.get_params': ('API/misc_tools.html#get_params', 'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.get_plot_groups': ('API/misc_tools.html#get_plot_groups', 'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.get_varname': ('API/misc_tools.html#get_varname', 'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.initialize_fig': ('API/misc_tools.html#initialize_fig', 'dabest/misc_tools.py'),
                                    'dabest.misc_tools.merge_two_dicts': ('API/misc_tools.html#merge_two_dicts', 'dabest/misc_tools.py'),
                                    'dabest.misc_tools.print_greeting': ('API/misc_tools.html#print_greeting', 'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.set_xaxis_ticks_and_lims': ( 'API/misc_tools.html#set_xaxis_ticks_and_lims',
+                                                                                   'dabest/misc_tools.py'),
+                                   'dabest.misc_tools.show_legend': ('API/misc_tools.html#show_legend', 'dabest/misc_tools.py'),
                                    'dabest.misc_tools.unpack_and_add': ('API/misc_tools.html#unpack_and_add', 'dabest/misc_tools.py')},
-            'dabest.plot_tools': { 'dabest.plot_tools.SwarmPlot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
+            'dabest.plot_tools': { 'dabest.plot_tools.DeltaDotsPlotter': ('API/plot_tools.html#deltadotsplotter', 'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.SwarmPlot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.SwarmPlot.__init__': ( 'API/plot_tools.html#swarmplot.__init__',
                                                                              'dabest/plot_tools.py'),
                                    'dabest.plot_tools.SwarmPlot._adjust_gutter_points': ( 'API/plot_tools.html#swarmplot._adjust_gutter_points',
@@ -82,14 +101,30 @@
                                                                                     'dabest/plot_tools.py'),
                                    'dabest.plot_tools.SwarmPlot._swarm': ('API/plot_tools.html#swarmplot._swarm', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.SwarmPlot.plot': ('API/plot_tools.html#swarmplot.plot', 'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.barplotter': ('API/plot_tools.html#barplotter', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.check_data_matches_labels': ( 'API/plot_tools.html#check_data_matches_labels',
                                                                                     'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.contrast_bars_plotter': ( 'API/plot_tools.html#contrast_bars_plotter',
+                                                                                'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.delta_text_plotter': ( 'API/plot_tools.html#delta_text_plotter',
+                                                                             'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.effect_size_curve_plotter': ( 'API/plot_tools.html#effect_size_curve_plotter',
+                                                                                    'dabest/plot_tools.py'),
                                    'dabest.plot_tools.error_bar': ('API/plot_tools.html#error_bar', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.get_swarm_spans': ('API/plot_tools.html#get_swarm_spans', 'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.grid_key_WIP': ('API/plot_tools.html#grid_key_wip', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.halfviolin': ('API/plot_tools.html#halfviolin', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.normalize_dict': ('API/plot_tools.html#normalize_dict', 'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.plot_minimeta_or_deltadelta_violins': ( 'API/plot_tools.html#plot_minimeta_or_deltadelta_violins',
+                                                                                              'dabest/plot_tools.py'),
                                    'dabest.plot_tools.sankeydiag': ('API/plot_tools.html#sankeydiag', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.single_sankey': ('API/plot_tools.html#single_sankey', 'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.slopegraph_plotter': ( 'API/plot_tools.html#slopegraph_plotter',
+                                                                             'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.summary_bars_plotter': ( 'API/plot_tools.html#summary_bars_plotter',
+                                                                               'dabest/plot_tools.py'),
+                                   'dabest.plot_tools.swarm_bars_plotter': ( 'API/plot_tools.html#swarm_bars_plotter',
+                                                                             'dabest/plot_tools.py'),
                                    'dabest.plot_tools.swarmplot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
                                    'dabest.plot_tools.width_determine': ('API/plot_tools.html#width_determine', 'dabest/plot_tools.py')},
             'dabest.plotter': {'dabest.plotter.effectsize_df_plotter': ('API/plotter.html#effectsize_df_plotter', 'dabest/plotter.py')}}}

dabest/_stats_tools/confint_1group.py

@@ -1,3 +1,5 @@
+"""A range of functions to compute bootstraps for a single sample."""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/confint_1group.ipynb.
 
 # %% auto 0

dabest/_stats_tools/confint_2group_diff.py

@@ -1,3 +1,5 @@
+"""A range of functions to compute bootstraps for the mean difference"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/confint_2group_diff.ipynb.
 
 # %% auto 0

dabest/_stats_tools/effsize.py

@@ -1,3 +1,5 @@
+"""A range of functions to compute various effect sizes."""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/effsize.ipynb.
 
 # %% ../../nbs/API/effsize.ipynb 4

dabest/forest_plot.py

@@ -1,3 +1,5 @@
+"""Creating forest plots from contrast objects."""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/forest_plot.ipynb.
 
 # %% auto 0