Merge branch 'propplot' into sankey

Adding proportion plot document into sankey branch

Author: Jacobluke-

dabest/_api.py

@@ -82,6 +82,16 @@ def load(data, idx=None, x=None, y=None, paired=None, id_col=None,
 
     >>> my_data = dabest.load(df, idx=("Control 1", "Test 1"))
 
+    For proportion plot.
+    >>> np.random.seed(88888)
+    >>> N = 10
+    >>> c1 = np.random.binomial(1, 0.2, size=N)
+    >>> t1 = np.random.binomial(1, 0.5, size=N)
+    >>> df = pd.DataFrame({'Control 1' : c1, 'Test 1': t1})
+    >>> my_data = dabest.load(df, idx=("Control 1", "Test 1"),proportional=True)
+
+
+
     '''
     from ._classes import Dabest
 

dabest/plotter.py

@@ -290,8 +290,8 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
 
     # Initialise the figure.
     # sns.set(context="talk", style='ticks')
-    init_fig_kwargs = dict(figsize=fig_size, dpi=plot_kwargs["dpi"])
-                           # ,tight_layout=True)
+    init_fig_kwargs = dict(figsize=fig_size, dpi=plot_kwargs["dpi"]
+                            ,tight_layout=True)
 
     width_ratios_ga = [2.5, 1]
     h_space_cummings = 0.3
@@ -365,7 +365,7 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
         contrast_axes = axx[1]
     rawdata_axes.set_frame_on(False)
     contrast_axes.set_frame_on(False)
-    fig.set_tight_layout(False)
+    # fig.set_tight_layout(False)
 
     redraw_axes_kwargs = {'colors'     : ytick_color,
                           'facecolors' : ytick_color,
@@ -484,9 +484,7 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
                                          **swarmplot_kwargs)
         else:
             # Plot the raw data as a barplot.
-            df_new = plot_data.copy()
-            bar1_df = df_new.groupby(xvar).count().reset_index()
-            bar1_df['proportion'] = [i / j for i, j in zip(bar1_df[yvar], bar1_df[yvar])]
+            bar1_df = pd.DataFrame({xvar: all_plot_groups, 'proportion': np.ones(len(all_plot_groups))})
             bar1 = sns.barplot(data=bar1_df, x=xvar, y="proportion",
                                ax=rawdata_axes,
                                order=all_plot_groups,
@@ -780,9 +778,9 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
         # Check that the effect size is within the swarm ylims.
         if effect_size_type in ["mean_diff", "cohens_d", "hedges_g","cohens_h"]:
             control_group_summary = plot_data.groupby(xvar)\
-                                             .mean().loc[current_control, yvar]
+                                             .mean(numeric_only=True).loc[current_control, yvar]
             test_group_summary = plot_data.groupby(xvar)\
-                                          .mean().loc[current_group, yvar]
+                                          .mean(numeric_only=True).loc[current_group, yvar]
         elif effect_size_type == "median_diff":
             control_group_summary = plot_data.groupby(xvar)\
                                              .median().loc[current_control, yvar]

dabest/tests/test_10_proportion_plot.py

@@ -55,20 +55,11 @@
 def test_101_gardner_altman_unpaired_propdiff():
     return two_groups_unpaired.mean_diff.plot();
 
-@pytest.mark.mpl_image_compare
-def test_102_gardner_altman_paired_propdiff():
-    return two_groups_paired.mean_diff.plot();
-
 @pytest.mark.mpl_image_compare
 def test_103_cummings_two_group_unpaired_propdiff():
     return two_groups_unpaired.mean_diff.plot(fig_size=(4, 6),
                                               float_contrast=False);
 
-@pytest.mark.mpl_image_compare
-def test_104_cummings_two_group_paired_propdiff():
-    return two_groups_paired.mean_diff.plot(fig_size=(6, 6),
-                                            float_contrast=False);
-
 @pytest.mark.mpl_image_compare
 def test_105_cummings_multi_group_unpaired__propdiff():
     return multi_2group.mean_diff.plot();

docs/source/_images/prop_1.png

@@ -143,7 +143,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static/css']
+html_static_path = ['_static']
 
 
 
@@ -228,4 +228,4 @@
 epub_exclude_files = ['search.html']
 
 def setup(app):
-    app.add_stylesheet('css/alabaster-custom.css')
+    app.add_css_file('css/alabaster-custom.css')