Return figure

ecell4/plotting/__init__.py

@@ -46,15 +46,17 @@ def plot_number_observer(*args, backend=None, **kwargs):
 
     """
     if backend == 'matplotlib':
-        _matplotlib.plot_number_observer(*args, **kwargs)
+        return _matplotlib.plot_number_observer(*args, **kwargs)
     elif backend == 'plotly':
         from . import _plotly
-        _plotly.plot_number_observer(*args, **kwargs)
+        return _plotly.plot_number_observer(*args, **kwargs)
     elif backend == 'elegans':
         from . import _elegans
         _elegans.plot_number_observer(*args, **kwargs)
     else:
-        BACKEND.plot_number_observer(*args, **kwargs)
+        ret = BACKEND.plot_number_observer(*args, **kwargs)
+        if ret is not None:
+            return ret
 
 def plot_world(*args, backend=None, **kwargs):
     """
@@ -75,15 +77,17 @@ def plot_world(*args, backend=None, **kwargs):
 
     """
     if backend == 'matplotlib':
-        _matplotlib.plot_world(*args, **kwargs)
+        return _matplotlib.plot_world(*args, **kwargs)
     elif backend == 'plotly':
         from . import _plotly
-        _plotly.plot_world(*args, **kwargs)
+        return _plotly.plot_world(*args, **kwargs)
     elif backend == 'elegans':
         from . import _elegans
         _elegans.plot_world(*args, **kwargs)
     else:
-        BACKEND.plot_world(*args, **kwargs)
+        ret = BACKEND.plot_world(*args, **kwargs)
+        if ret is not None:
+            return ret
 
 def plot_movie(*args, backend=None, **kwargs):
     """
@@ -125,15 +129,17 @@ def plot_trajectory(*args, backend=None, **kwargs):
 
     """
     if backend == 'matplotlib':
-        _matplotlib.plot_trajectory(*args, **kwargs)
+        return _matplotlib.plot_trajectory(*args, **kwargs)
     elif backend == 'plotly':
         from . import _plotly
-        _plotly.plot_trajectory(*args, **kwargs)
+        return _plotly.plot_trajectory(*args, **kwargs)
     elif backend == 'elegans':
         from . import _elegans
         _elegans.plot_trajectory(*args, **kwargs)
     else:
-        BACKEND.plot_trajectory(*args, **kwargs)
+        ret = BACKEND.plot_trajectory(*args, **kwargs)
+        if ret is not None:
+            return ret
 
 plot_movie_of_trajectory = _matplotlib.plot_movie_of_trajectory_with_matplotlib  # default
 

ecell4/plotting/_matplotlib.py

@@ -164,9 +164,10 @@ def plot_number_observer(
         ax.set_ylim(ylim)
 
     if filename is not None:
-        plt.savefig(filename)
-    else:
-        plt.show()
+        raise RuntimeError("filename was deprecated. Use the return value.")
+        # plt.savefig(filename)
+    plt.close()
+    return fig
 
 plot_number_observer_with_matplotlib = plot_number_observer
 
@@ -274,7 +275,8 @@ def plot_world(
             legend_opts.update(legend)
         ax.legend(handles=plots, labels=species_list,  **legend_opts)
 
-    plt.show()
+    plt.close()
+    return fig
 
 plot_world_with_matplotlib = plot_world
 
@@ -331,7 +333,8 @@ def plot_trajectory(
         if isinstance(legend, dict):
             legend_opts.update(legend)
         ax.legend(**legend_opts)
-    plt.show()
+    plt.close()
+    return fig
 
 plot_trajectory_with_matplotlib = plot_trajectory
 
@@ -438,7 +441,8 @@ def plot_trajectory2d_with_matplotlib(
         if isinstance(legend, dict):
             legend_opts.update(legend)
         ax.legend(**legend_opts)
-    plt.show()
+    plt.close()
+    return fig
 
 def plot_movie_of_trajectory2d_with_matplotlib(
         obs, plane='xy', figsize=6, grid=True,
@@ -839,8 +843,8 @@ def plot_world2d_with_matplotlib(
             legend_opts.update(legend)
         ax.legend(**legend_opts)
         # ax.legend(handles=plots, labels=species_list,  **legend_opts)
-
-    plt.show()
+    plt.close()
+    return fig
 
 def __scatter_world2d_with_matplotlib(
         world, indices, ax, species_list, marker_size, max_count, scale, **kwargs):

ecell4/plotting/_plotly.py

@@ -105,8 +105,7 @@ def plot_number_observer(
     if layout is not None:
         layout_.update(layout)
     fig.update(dict(layout=layout_))
-
-    plotly.offline.iplot(fig)
+    return fig
 
 plot_number_observer_with_plotly = plot_number_observer
 
@@ -142,8 +141,7 @@ def plot_stl(filename, layout=None, **kwargs):
         layout_.update(layout)
     layout_ = go.Layout(**layout_)
     fig = go.Figure(data=[mesh3D], layout=layout_)
-    plotly.offline.iplot(fig)
-
+    return fig
 
 def plot_world(world, species_list=None, max_count=1000, marker=None, layout=None, stl=None):
     """
@@ -215,7 +213,7 @@ def plot_world(world, species_list=None, max_count=1000, marker=None, layout=Non
         layout_.update(layout)
     layout_ = go.Layout(**layout_)
     fig = go.Figure(data=traces, layout=layout_)
-    plotly.offline.iplot(fig)
+    return fig
 
 plot_world_with_plotly = plot_world
 
@@ -268,6 +266,6 @@ def plot_trajectory(
         layout_.update(layout)
     layout_ = go.Layout(**layout_)
     fig = go.Figure(data=traces, layout=layout_)
-    plotly.offline.iplot(fig)
+    return fig
 
 plot_trajectory_with_plotly = plot_trajectory