Adding gridkey implementation

Author: maiyishan

dabest/_classes.py

@@ -2445,6 +2445,11 @@ def plot(self, color_col=None,
             fig_size=None,
             dpi=100,
             ax=None,
+             
+            gridkey_rows=None,
+            gridkey_merge_pairs = False,
+            gridkey_show_Ns = True,
+            gridkey_show_es = True,
 
             swarmplot_kwargs=None,
             barplot_kwargs=None,
@@ -2536,6 +2541,10 @@ def plot(self, color_col=None,
         ax : matplotlib.Axes, default None
             Provide an existing Axes for the plots to be created. If no Axes is
             specified, a new matplotlib Figure will be created.
+        gridkey_rows : list, default None
+            Provide a list of row labels for the gridkey. The supplied idx is
+            checked against the row labels to determine whether the corresponding
+            cell should be populated or not.
         swarmplot_kwargs : dict, default None
             Pass any keyword arguments accepted by the seaborn `swarmplot`
             command here, as a dict. If None, the following keywords are

dabest/plotter.py

@@ -30,6 +30,7 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
         fig_size=None,
         dpi=100,
         ax=None,
+        gridkey_rows=None,
         swarmplot_kwargs=None,
         violinplot_kwargs=None,
         slopegraph_kwargs=None,
@@ -65,6 +66,7 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
 
     ytick_color = plt.rcParams["ytick.color"]
     face_color = plot_kwargs["face_color"]
+
     if plot_kwargs["face_color"] is None:
         face_color = "white"
 
@@ -175,6 +177,16 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
     else:
         legend_kwargs = merge_two_dicts(default_legend_kwargs,
                                         plot_kwargs["legend_kwargs"])
+        
+        
+################################################### GRIDKEY WIP - extracting kwargs      
+    
+    gridkey_rows = plot_kwargs["gridkey_rows"]
+    gridkey_merge_pairs = plot_kwargs["gridkey_merge_pairs"]
+    gridkey_show_Ns = plot_kwargs["gridkey_show_Ns"]
+    gridkey_show_es = plot_kwargs["gridkey_show_es"]
+    
+################################################### END GRIDKEY WIP - extracting kwargs
 
     # Group summaries kwargs.
     gs_default = {'mean_sd', 'median_quartiles', None}
@@ -298,7 +310,17 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
                             ,tight_layout=True)
 
     width_ratios_ga = [2.5, 1]
-    h_space_cummings = 0.3
+    
+###################### GRIDKEY HSPACE ALTERATION
+
+    # Sets hspace for cummings plots if gridkey is shown.
+    if gridkey_rows is not None:
+        h_space_cummings = 0.1
+    else:
+        h_space_cummings = 0.3
+        
+###################### END GRIDKEY HSPACE ALTERATION        
+        
     if plot_kwargs["ax"] is not None:
         # New in v0.2.6.
         # Use inset axes to create the estimation plot inside a single axes.
@@ -355,7 +377,7 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
 
         else:
             fig, axx = plt.subplots(nrows=2,
-                                    gridspec_kw={"hspace": 0.3},
+                                    gridspec_kw={"hspace": h_space_cummings},
                                     **init_fig_kwargs)
             fig.patch.set_facecolor(face_color)
             # If the contrast axes are NOT floating, create lists to store
@@ -643,6 +665,7 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
         contrast_axes.plot([tick], current_effsize, marker='o',
                            color=ytick_color,
                            markersize=es_marker_size)
+        
         # Plot the confidence interval.
         contrast_axes.plot([tick, tick],
                            [current_ci_low, current_ci_high],
@@ -1113,6 +1136,124 @@ def EffectSizeDataFramePlotter(EffectSizeDataFrame, **plot_kwargs):
                          og_ylim_delta[0], og_ylim_delta[1],
                          **redraw_axes_kwargs)
 
+
+################################################### GRIDKEY MAIN CODE WIP
+    
+    #if gridkey_rows is None, skip everything here
+    if gridkey_rows is not None:
+        
+        # Raise error if there are more than 2 items in any idx and gridkey_merge_pairs is True and is_paired is not None
+        if gridkey_merge_pairs is True and is_paired is not None:
+            for i in idx:
+                if len(i) > 2:
+                    warnings.warn("gridkey_merge_pairs=True only works if all idx in tuples have only two items. gridkey_merge_pairs has automatically been set to False")
+                    gridkey_merge_pairs = False
+                    break
+        elif gridkey_merge_pairs is True and is_paired is None:
+            warnings.warn("gridkey_merge_pairs=True is only applicable for paired data.")
+            gridkey_merge_pairs = False
+                    
+        # Checks for gridkey_merge_pairs and is_paired; if both are true, "merges" the gridkey per pair
+        if gridkey_merge_pairs is True and is_paired is not None:          
+            groups_for_gridkey = []
+            for i in idx:
+                groups_for_gridkey.append(i[1])
+        else:
+            groups_for_gridkey = all_plot_groups
+                    
+        
+        # raise errors if gridkey_rows is not a list, or if the list is empty
+        if isinstance(gridkey_rows, list) is False:
+            raise TypeError("gridkey_rows must be a list.")
+        elif len(gridkey_rows) == 0:
+            raise ValueError("gridkey_rows cannot be an empty list.")
+        
+        
+        # raise Warning if an item in gridkey_rows is not contained in any idx
+        for i in gridkey_rows:
+            in_idx = 0
+            for j in groups_for_gridkey:
+                if i in j:
+                    in_idx += 1
+            if in_idx == 0:
+                if is_paired is not None:
+                    warnings.warn(i + " is not in any idx. Please check. Alternatively, merging gridkey pairs may not be suitable for your data; try passing gridkey_merge_pairs=False.")
+                else:
+                    warnings.warn(i + " is not in any idx. Please check.")   
+        
+        
+        # Populate table: checks if idx for each column contains rowlabel name
+        # IF so, marks that element as present w black dot, or space if not present
+        table_cellcols = []   
+        for i in gridkey_rows:
+            thisrow = []
+            for q in groups_for_gridkey:
+                if str(i) in q:
+                    thisrow.append(u"\u25CF")
+                else:
+                    thisrow.append("")
+            table_cellcols.append(thisrow)
+        
+        
+        # Adds a row for Ns with the Ns values
+        if gridkey_show_Ns == True:
+            gridkey_rows.append("Ns")
+            list_of_Ns = []
+            for i in groups_for_gridkey:
+                list_of_Ns.append(str(counts.loc[i]))
+            table_cellcols.append(list_of_Ns)
+
+            
+        # Adds a row for effectsizes with effectsize values
+        if gridkey_show_es == True:
+            gridkey_rows.append(u"\u0394")
+            effsize_list = []
+            results_list = results.test.to_list()
+        
+            # get the effect size, append + or -, 2 dec places
+            for i in enumerate(groups_for_gridkey):
+                if i[1] in results_list:
+                    curr_esval = results.loc[results["test"] == i[1]]["difference"].iloc[0]
+                    if curr_esval >= 0: 
+                        curr_esval_str = "+" + str("%.2f" % curr_esval)
+                    else:
+                        curr_esval_str = str("%.2f" % curr_esval)
+                    effsize_list.append(curr_esval_str)
+                else:
+                    effsize_list.append("-")
+                    
+            table_cellcols.append(effsize_list)
+        
+        # If Gardner-Altman plot, plot on raw data and not contrast axes
+        if float_contrast == True:
+            axes_ploton = rawdata_axes
+        else:
+            axes_ploton = contrast_axes
+        
+        # Account for extended x axis in case of show_delta2 or show_mini_meta
+        x_groups_for_width = len(groups_for_gridkey)
+        if show_delta2 is True or show_mini_meta is True:
+              x_groups_for_width += 2                 
+        gridkey_width = len(groups_for_gridkey) / x_groups_for_width
+        
+        gridkey = axes_ploton.table(cellText = table_cellcols, 
+                                    rowLabels = gridkey_rows, 
+                                    cellLoc = "center",
+                                    bbox = [0, -len(gridkey_rows)*0.1-0.05, gridkey_width, len(gridkey_rows)*0.1],
+                                    **{"alpha" : 0.5})   
+        
+        # modifies row label cells
+        for cell in gridkey._cells:
+            if cell[1] == -1:
+                gridkey._cells[cell].visible_edges = "open"
+                gridkey._cells[cell].set_text_props(**{ "ha" : "right" }) 
+                
+        # turns off both x axes
+        rawdata_axes.get_xaxis().set_visible(False)
+        contrast_axes.get_xaxis().set_visible(False)
+        
+ ####################################################### END GRIDKEY MAIN CODE WIP       
+        
     # Make sure no stray ticks appear!
     rawdata_axes.xaxis.set_ticks_position('bottom')
     rawdata_axes.yaxis.set_ticks_position('left')

nbs/API/class.ipynb

@@ -3257,6 +3257,11 @@
     "            fig_size=None,\n",
     "            dpi=100,\n",
     "            ax=None,\n",
+    "             \n",
+    "            gridkey_rows=None,\n",
+    "            gridkey_merge_pairs = False,\n",
+    "            gridkey_show_Ns = True,\n",
+    "            gridkey_show_es = True,\n",
     "\n",
     "            swarmplot_kwargs=None,\n",
     "            barplot_kwargs=None,\n",
@@ -3348,6 +3353,10 @@
     "        ax : matplotlib.Axes, default None\n",
     "            Provide an existing Axes for the plots to be created. If no Axes is\n",
     "            specified, a new matplotlib Figure will be created.\n",
+    "        gridkey_rows : list, default None\n",
+    "            Provide a list of row labels for the gridkey. The supplied idx is\n",
+    "            checked against the row labels to determine whether the corresponding\n",
+    "            cell should be populated or not.\n",
     "        swarmplot_kwargs : dict, default None\n",
     "            Pass any keyword arguments accepted by the seaborn `swarmplot`\n",
     "            command here, as a dict. If None, the following keywords are\n",