How to make Matplotlib scatterplots transparent as a group?

Question

I'm making some scatterplots using Matplotlib (python 3.4.0, matplotlib 1.4.3, running on Linux Mint 17). It's easy enough to set alpha transparency for each point individually; is there any way to set them as a group, so that two overlapping points from the same group don't change the color?

Example code:

import matplotlib.pyplot as plt import numpy as np  def points(n=100):     x = np.random.uniform(size=n)     y = np.random.uniform(size=n)     return x, y x1, y1 = points() x2, y2 = points() fig = plt.figure(figsize=(4,4)) ax = fig.add_subplot(111, title="Test scatter") ax.scatter(x1, y1, s=100, color="blue", alpha=0.5) ax.scatter(x2, y2, s=100, color="red", alpha=0.5) fig.savefig("test_scatter.png") 

Results in this output:

but I want something more like this one:

I can workaround by saving as SVG and manually grouping then in Inkscape, then setting transparency, but I'd really prefer something I can code. Any suggestions?

Answer 1

Yes, interesting question. You can get this scatterplot with Shapely. Here is the code :

import matplotlib.pyplot as plt import matplotlib.patches as ptc import numpy as np from shapely.geometry import Point from shapely.ops import cascaded_union  n = 100 size = 0.02 alpha = 0.5  def points():     x = np.random.uniform(size=n)     y = np.random.uniform(size=n)     return x, y  x1, y1 = points() x2, y2 = points() polygons1 = [Point(x1[i], y1[i]).buffer(size) for i in range(n)] polygons2 = [Point(x2[i], y2[i]).buffer(size) for i in range(n)] polygons1 = cascaded_union(polygons1) polygons2 = cascaded_union(polygons2)  fig = plt.figure(figsize=(4,4)) ax = fig.add_subplot(111, title="Test scatter") for polygon1 in polygons1:     polygon1 = ptc.Polygon(np.array(polygon1.exterior), facecolor="red", lw=0, alpha=alpha)     ax.add_patch(polygon1) for polygon2 in polygons2:     polygon2 = ptc.Polygon(np.array(polygon2.exterior), facecolor="blue", lw=0, alpha=alpha)     ax.add_patch(polygon2) ax.axis([-0.2, 1.2, -0.2, 1.2])  fig.savefig("test_scatter.png") 

and the result is :