Allow to set contour levels at quantiles instead of KDE fractions (close

 #180)

CHANGELOG

@@ -1,4 +1,5 @@
 0.9.2
+ - Allow to set contour levels at quantiles instead of KDE fractions (#180)
  - Allow to manually select contour levels
  - Pin numpy version to <=1.13.0 to prevent ValueError caused
    by chaco testing whether an array object is contained in another

docs/sec_interface.rst

@@ -352,7 +352,13 @@ Scatter plot:
 Contour plot:
   Enable or disable contour plots, modify contour plot parameters,
   and select the title and color for each scatter plot.
-
+
+  .. versionadded:: 0.9.2
+
+    Contour lines can now be plotted at KDE data quantiles (percentiles/100)
+    instead of at fractions of the overall KDE using the
+    `contour level mode` option. A contour line at a 0.95 quantile
+    contains 5% of all data points.
 
 
 .. _ui_expert:

shapeout/gui/confparms.py

@@ -38,8 +38,7 @@ def get_config_entry_choices(key, subkey, ignore_axes=[]):
         elif subkey == "isoelastics":
             choices = ["not shown", "analytical", "numerical", "legacy"]
         elif subkey == "contour level mode":
-            choices = ["fraction"]
-            #choices = ["fraction", "quantile"]
+            choices = ["fraction", "quantile"]
     elif key == "analysis":
         if subkey == "regression model":
             choices = ["lmm", "glmm"]

shapeout/gui/plot_contour.py

@@ -153,8 +153,10 @@ def set_contour_data(plot, analysis):
         if mode == "fraction":
             plev = list(np.nanmax(density) * levels)
         elif mode == "quantile":
-            raise NotImplementedError("TODO")
-            #plev = list(np.nanpercentile(density, q=levels*100))
+            pdensity = mm.get_kde_scatter(xax=xax, yax=yax,
+                                          kde_type=kde_type,
+                                          kde_kwargs=kde_kwargs)
+            plev = list(np.nanpercentile(pdensity, q=levels*100))
         else:
             raise ValueError("Unknown contour level mode `{}`!".format(mode))