I'm trying to make a 3d scatterplot with fading points over time, similar to this question. However, when I apply the colormap to the data, then the face of the marker changes color but the edge remains solid.
I've tried using the edgecolors='None', edgecolor='none' kwargs, the marker='o' kwarg as per this example, and the edgecolor='face' kwarg. I've also tried using post creation methods such as scat3D.set_edgecolor("None") etc. The first attempts throw an error, and the latter have no effect.
Error from setting kwargs:
Traceback (most recent call last):
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 230, in saving
yield self
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 1156, in save
writer.grab_frame(**savefig_kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 384, in grab_frame
dpi=self.dpi, **savefig_kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/figure.py", line 2180, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backends/backend_qt5agg.py", line 88, in print_figure
super().print_figure(*args, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2082, in print_figure
**kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 442, in print_raw
FigureCanvasAgg.draw(self)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 388, in draw
self.figure.draw(self.renderer)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/figure.py", line 1709, in draw
renderer, self, artists, self.suppressComposite)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/image.py", line 135, in _draw_list_compositing_images
a.draw(renderer)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 292, in draw
reverse=True)):
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 291, in <lambda>
key=lambda col: col.do_3d_projection(renderer),
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 545, in do_3d_projection
ecs = (_zalpha(self._edgecolor3d, vzs) if self._depthshade else
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 847, in _zalpha
rgba = np.broadcast_to(mcolors.to_rgba_array(colors), (len(zs), 4))
File "<__array_function__ internals>", line 6, in broadcast_to
File "/home/max/.local/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 182, in broadcast_to
return _broadcast_to(array, shape, subok=subok, readonly=True)
File "/home/max/.local/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 127, in _broadcast_to
op_flags=['readonly'], itershape=shape, order='C')
ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (0,4) and requested shape (100,4)
(There's a during the handling the above exception another occured error after that, but my post was flagged as spam so I didn't include it)
Here's the code without the error (adding a kwarg listed above causes the error):
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.animation as animation
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.patches as mpatches
total = 10
num_whatever = 100
to_plot = [np.random.rand(num_whatever, 3) for i in range(total)]
colors = np.linspace(0, 1, num_whatever)
fig = plt.figure()
ax3d = Axes3D(fig)
scat3D = ax3d.scatter([],[],[], s=10, cmap="Blues", vmin=0, vmax=1)
scat3D.set_cmap("Blues") # cmap argument above is ignored, so set it manually
ttl = ax3d.text2D(0.05, 0.95, "", transform=ax3d.transAxes)
def update_plot(i):
print( i, to_plot[i].shape)
ttl.set_text('PCA on 3 components at step = {}'.format(i*20))
scat3D._offsets3d = np.transpose(to_plot[i])
scat3D.set_array(colors)
return scat3D,
def init():
scat3D.set_offsets([[],[],[]])
plt.style.use('ggplot')
ani = animation.FuncAnimation(fig, update_plot, init_func=init,
blit=False, interval=300, frames=range(total))
ani.save("ani.gif", writer="imagemagick")
plt.show()
Here's the plot with the marker edges not hidden:
You can see that the faded points still have the marker edges not colormapped. I would expect that setting edgecolor would be unnecessary in the first place, since the 2d animation clearly doesn't need it. But why would adding that kwarg cause me to get a operands could not be broadcast togeather error? I don't have any array with shape (0, 4), so it's not clear where this is coming from.
