Add native support for stacked area charts

This commit introduces similar stacked area charts to
`epi.plots.web.stacked()` in `epi.plots.native`, this adding native
support for stacked area charts.

Changelist:
- Add `epi.plots.native.stacked()`
- Add testing support for ^ in `tests/plotting`

Additional Notes:
Warnings (minor):
Occasionally, legend visibility is poor due to the fact that
`matplotlib` does not enforce any white background on the legend.
A patch will likely fix this.

epispot/plots/native.py

@@ -96,3 +96,72 @@ def model(Model, time_frame, title='Compartment Populations over Time',
     plt.legend()
 
     return plt
+
+
+def stacked(Model, time_frame, title='Compartment Populations over Time',
+          starting_state=None, compartments=None, names=None, show_susceptible=False,
+          log=False, latex=True):
+    """
+    Plots the results of one model using `matplotlib`.
+    The results are displayed natively via a `matplotlib` window as a stacked area chart.
+    There are various ways to customize the generated plots by modifying
+    the time frame or compartments displayed. 
+    Additionally, `matplotlib` allows editing plots even after 
+    they have been created to change things like colors, margins, etc.
+
+    - Model: An `epispot.models.Model` object
+    - time_frame: A `range()` describing the time period to plot
+    - title: (`='Compartment Populations over Time`) The title of the plot
+    - starting_state: (default:inherited) Initial model state (see `epispot.models.Model.integrate` parameter `starting_state`)
+    - compartments: (default:all) The indices of the compartments in the model to plot; 
+                    all other compartments will be hidden
+    - names: (default:`Model.layer_names`) A list of names for each of the compartments
+    - show_susceptible: (`=False`) Boolean value describing whether or not to plot the Susceptible compartment.\
+                                   **This assumes that the Susceptible compartment is the first in `Model`**\
+                                   Note:\
+                                   > This can potentially result in less visibility for other compartments
+                                   > since usually the Susceptible compartment comprises of many, many
+                                   > more individuals than the other compartments combined.
+    - log: (`=False`) Boolean value indicating whether or not to use a logarithmic scale when plotting `Model`
+    - latex: (`=True`) Turn off if you do not have LaTeX installed or want quicker loading times
+    - return: `pyplot` figure (display with `.show()`)
+    """
+
+    if latex:
+        plt.style.use('science')
+
+    DataFrame = {}
+    System = Model.integrate(time_frame, starting_state=starting_state)
+
+    # parameter substitutions
+    if compartments is None:
+        compartments = list(range(len(Model.layers)))
+
+    if names is None:
+        names = Model.layer_names
+
+    # setup
+    for name in Model.layer_names:
+        DataFrame[name] = []
+
+    for day in System:
+        for i, compartment in enumerate(day):
+            DataFrame[Model.layer_names[i]].append(compartment)
+
+    if not show_susceptible:
+        for i, compartment in enumerate(compartments):
+            if compartment == 0:
+                del compartments[i]
+                break
+
+    # plotting
+    plt.figure(figsize=(9, 5))
+    plt.stackplot(time_frame, *[DataFrame[Model.layer_names[compartment]] for compartment in compartments], 
+                  labels=[names[compartment] for compartment in compartments])
+
+    if log:
+        plt.yscale('log')
+    plt.title(title)
+    plt.legend(loc='upper left', facecolor='white')
+
+    return plt

tests/test_plotting.py

@@ -16,6 +16,9 @@
    |- native
       |- plain
       |- full
+   |- native-stack
+      |- plain
+      |- full
 """
 
 import epispot as epi
@@ -115,3 +118,25 @@ def test_full_native():
                                     show_susceptible=True, 
                                     log=True)
     return Figure
+
+
+def test_plain_native_stack():
+    Model = epi.pre.SEIR(R_0, N, place, gamma, delta)  # compile model
+    Figure = epi.plots.native.stacked(Model, range(120), latex=False)  # `latex=False` flag speeds up testing
+    return Figure
+
+
+def test_full_native_stack():
+    Model = epi.pre.SEIR(R_0, N, place, gamma, delta)  # compile model
+    #`latex=True` enabled by default
+    # blank strings `''` in `names=` are used to indicate that
+    # the corresponding compartment is not being plotted
+    Figure = epi.plots.native.stacked(Model, range(120),
+                                    title='SEIR Model Plot',
+                                    starting_state=[N(0) - 50, 25, 25, 0],
+                                    compartments=[0, 3],
+                                    names=['Susceptible Population',
+                                           '', '', 'Removed/Recovered'],
+                                    show_susceptible=True,
+                                    log=True)
+    return Figure