Add example for concurrences

.gitignore

@@ -1,6 +1,7 @@
 dask-worker-space
 # netcdf outputs
 *nc
+.pytest_cache
 
 contact_map/version.py
 cover

contact_map/concurrence.py

@@ -223,9 +223,12 @@ def x_values(self):
     def x_values(self, x_values):
         self._x_values = x_values
 
-    def plot(self, concurrence=None):
+    def plot(self, concurrence=None, **kwargs):
         """Contact concurrence plot based on matplotlib
 
+        Additional kwargs given here will be passed to the matplotlib
+        ``Axes.plot()`` method.
+
         Parameters
         ----------
         concurrence : :class:`.Concurrence`
@@ -249,23 +252,30 @@ def plot(self, concurrence=None):
         fig = plt.figure(1)
         ax = fig.add_subplot(111)
 
+        plot_kwargs = {'markersize': 1}
+        plot_kwargs.update(kwargs)
+
         y_val = -1.0
         for label, val_set in zip(labels, concurrence.values):
             x_vals = [x for (x, y) in zip(x_values, val_set) if y]
-            ax.plot(x_vals, [y_val] * len(x_vals), '.', markersize=1,
-                    label=label)
+            ax.plot(x_vals, [y_val] * len(x_vals), '.', label=label,
+                    **plot_kwargs)
             y_val -= 1.0
 
         ax.set_ylim(top=0.0)
         ax.set_xlim(left=min(x_values), right=max(x_values))
+        ax.set_yticks([])
         lgd = ax.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
         return (fig, ax, lgd)
 
 
-def plot_concurrence(concurrence, labels=None, x_values=None):  # -no-cov-
+def plot_concurrence(concurrence, labels=None, x_values=None, **kwargs):  # -no-cov-
     """
     Convenience function for concurrence plots.
 
+    Additional kwargs given here will be passed to the matplotlib
+    ``Axes.plot()`` method.
+
     Parameters
     ----------
     concurrence : :class:`.Concurrence`
@@ -279,4 +289,4 @@ def plot_concurrence(concurrence, labels=None, x_values=None):  # -no-cov-
     --------
     :class:`.ConcurrencePlotter`
     """
-    return ConcurrencePlotter(concurrence, labels, x_values).plot()
+    return ConcurrencePlotter(concurrence, labels, x_values).plot(**kwargs)

docs/examples/index.rst

@@ -1,8 +1,10 @@
 Examples
 ========
 
-So far, we only have one major example. We will add others here as they
-are written.
+We have several examples to illustrate various features of the code. These
+notebooks have been rendered here for the web, but the originals are
+found in the ``examples/`` directory of the package, and you can run them
+yourself!
 
 .. toctree::
     :maxdepth: 1

docs/installing.rst

@@ -97,6 +97,19 @@ This is a three-step process:
    interpreted uses) and the ``.`` tells it to find ``setup.py`` in the
    current directory.
 
+Additional functionality
+========================
+
+Installing some additional packages will immediately enable additional
+features in ``contact_map``. To get all the functionality, install the
+packages in ``optional_installs.txt``, either with ``pip install -r
+optional_installs.txt`` or ``conda install -y --file
+optional_installs.txt``.
+
+Specific extra functionality that can be enabled:
+
+* plotting tools (install ``matplotlib``)
+* parallelization (install ``dask``, ``distributed``)
 
 Testing your installation
 =========================