upgrade matplotlib

README.md

@@ -73,7 +73,7 @@ source ~/.bashrc
 ~~~
 
 ## Inputs
-_`Note: Support for the BIOM format has been dropped (temporarily) in OPAL 1.0.4 due to incompatibility with Python 3.7.*.`_
+_**`Note: Support for the BIOM format has been dropped (temporarily) in OPAL 1.0.4 due to incompatibility with Python 3.7.*.`**_
 
 OPAL uses at least two files:
 1. A gold standard taxonomic profile

requirements/default.txt

@@ -1,5 +1,5 @@
 numpy==1.16.4
-matplotlib==2.0.2
+matplotlib==3.1.1
 dendropy==4.4.0
 pandas==0.24.2
 h5py==2.9.0

src/html_opal.py

@@ -47,7 +47,7 @@ def create_heatmap_bar(output_dir):
     # hide heatmap
     pltx.gca().set_visible(False)
 
-    fig.savefig(os.path.join(output_dir, 'heatmap_bar.png'), dpi=100, format='png', bbox_inches='tight', pad_inches=-.035, transparent=True)
+    fig.savefig(os.path.join(output_dir, 'heatmap_bar.png'), dpi=100, format='png', bbox_inches='tight', pad_inches=-.001, transparent=True)
     pltx.close(fig)
 
 

src/plots.py

@@ -358,7 +358,7 @@ def spider_plot(metrics, labels, rank_to_metric_to_toolvalues, output_dir, file_
     fig, axes = plt.subplots(figsize=(9, 9), nrows=2, ncols=3, subplot_kw=dict(projection='radar'))
     fig.subplots_adjust(wspace=0.35, hspace=0.05, top=0.87, bottom=0.3)
 
-    for ax, rank in zip(axes.flatten(), c.PHYLUM_SPECIES):
+    for ax, rank in zip(axes.flat, c.PHYLUM_SPECIES):
         if grid_points:
             ax.set_rgrids(grid_points, fontsize='xx-small')
         else:
@@ -385,15 +385,19 @@ def spider_plot(metrics, labels, rank_to_metric_to_toolvalues, output_dir, file_
             it += 1
         ax.set_varlabels(labels)
 
-        ax.set_ylim([0.0, 1.0])
-        ax.set_xlim([0.0, 1.0])
+        ax.set_rmax(1)
 
         # color red label of tools without a value for at least one metric
         xticklabels = ax.get_xticklabels()
         for metric in metric_to_toolindex:
             for toolindex in metric:
                 xticklabels[toolindex].set_color([1, 0, 0])
 
+        # move ticks labels closer to plot and set font size
+        for xticklabel in xticklabels:
+            xticklabel.set_position((.1,.1))
+            xticklabel.set_fontsize('small')
+
     ax = axes[0, 0]
     ax.legend(metrics, loc=(1.6 - 0.353 * len(metrics), 1.3), labelspacing=0.1, fontsize='small', ncol=len(metrics))
     fig.savefig(os.path.join(output_dir, file_name + '.pdf'), dpi=100, format='pdf', bbox_inches='tight')

src/utils/spider_plot_functions.py

@@ -2,11 +2,12 @@
 
 import matplotlib
 matplotlib.use('Agg')
-import matplotlib.pyplot as plt
+from matplotlib.patches import Circle, RegularPolygon
 from matplotlib.path import Path
-from matplotlib.spines import Spine
 from matplotlib.projections.polar import PolarAxes
 from matplotlib.projections import register_projection
+from matplotlib.spines import Spine
+from matplotlib.transforms import Affine2D
 
 
 def radar_factory(num_vars, frame='circle'):
@@ -24,37 +25,25 @@ def radar_factory(num_vars, frame='circle'):
     """
     # calculate evenly-spaced axis angles
     theta = np.linspace(0, 2*np.pi, num_vars, endpoint=False)
-    # rotate theta such that the first axis is at the top
-    theta += np.pi/2
-
-    def draw_poly_patch(self):
-        verts = unit_poly_verts(theta)
-        return plt.Polygon(verts, closed=True, edgecolor='k')
-
-    def draw_circle_patch(self):
-        # unit circle centered on (0.5, 0.5)
-        return plt.Circle((0.5, 0.5), 0.5)
-
-    patch_dict = {'polygon': draw_poly_patch, 'circle': draw_circle_patch}
-    if frame not in patch_dict:
-        raise ValueError('unknown value for `frame`: %s' % frame)
 
     class RadarAxes(PolarAxes):
 
         name = 'radar'
         # use 1 line segment to connect specified points
         RESOLUTION = 1
-        # define draw_frame method
-        draw_patch = patch_dict[frame]
 
-        def fill(self, *args, **kwargs):
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, **kwargs)
+            # rotate plot such that the first axis is at the top
+            self.set_theta_zero_location('N')
+
+        def fill(self, *args, closed=True, **kwargs):
             """Override fill so that line is closed by default"""
-            closed = kwargs.pop('closed', True)
-            return super(RadarAxes, self).fill(closed=closed, *args, **kwargs)
+            return super().fill(closed=closed, *args, **kwargs)
 
         def plot(self, *args, **kwargs):
             """Override plot so that line is closed by default"""
-            lines = super(RadarAxes, self).plot(*args, **kwargs)
+            lines = super().plot(*args, **kwargs)
             for line in lines:
                 self._close_line(line)
 
@@ -67,37 +56,35 @@ def _close_line(self, line):
                 line.set_data(x, y)
 
         def set_varlabels(self, labels):
-            self.set_thetagrids(np.degrees(theta), labels, fontsize='small')
+            return self.set_thetagrids(np.degrees(theta), labels)
 
         def _gen_axes_patch(self):
-            return self.draw_patch()
+            # The Axes patch must be centered at (0.5, 0.5) and of radius 0.5
+            # in axes coordinates.
+            if frame == 'circle':
+                return Circle((0.5, 0.5), 0.5)
+            elif frame == 'polygon':
+                return RegularPolygon((0.5, 0.5), num_vars,
+                                      radius=.5, edgecolor="k")
+            else:
+                raise ValueError("unknown value for 'frame': %s" % frame)
 
         def _gen_axes_spines(self):
             if frame == 'circle':
-                return PolarAxes._gen_axes_spines(self)
-            # The following is a hack to get the spines (i.e. the axes frame)
-            # to draw correctly for a polygon frame.
-
-            # spine_type must be 'left', 'right', 'top', 'bottom', or `circle`.
-            spine_type = 'circle'
-            verts = unit_poly_verts(theta)
-            # close off polygon by repeating first vertex
-            verts.append(verts[0])
-            path = Path(verts)
-
-            spine = Spine(self, spine_type, path)
-            spine.set_transform(self.transAxes)
-            return {'polar': spine}
+                return super()._gen_axes_spines()
+            elif frame == 'polygon':
+                # spine_type must be 'left'/'right'/'top'/'bottom'/'circle'.
+                spine = Spine(axes=self,
+                              spine_type='circle',
+                              path=Path.unit_regular_polygon(num_vars))
+                # unit_regular_polygon gives a polygon of radius 1 centered at
+                # (0, 0) but we want a polygon of radius 0.5 centered at (0.5,
+                # 0.5) in axes coordinates.
+                spine.set_transform(Affine2D().scale(.5).translate(.5, .5)
+                                    + self.transAxes)
+                return {'polar': spine}
+            else:
+                raise ValueError("unknown value for 'frame': %s" % frame)
 
     register_projection(RadarAxes)
     return theta
-
-
-def unit_poly_verts(theta):
-    """Return vertices of polygon for subplot axes.
-
-    This polygon is circumscribed by a unit circle centered at (0.5, 0.5)
-    """
-    x0, y0, r = [0.5] * 3
-    verts = [(r*np.cos(t) + x0, r*np.sin(t) + y0) for t in theta]
-    return verts

version.py

@@ -1 +1 @@
-__version__ = '1.0.4'
+__version__ = '1.0.5'