如何在 matplotlib 中制作不透明散射 plot

Question

When making a scatter plot in matplotlib, I found that when I change the size of the dots, they become transparent. How can I prevent this from happening?

I've already tried alpha=1 , facecolor='k' but none of these seem to work

Example code

X = np.random.normal(0,1,5000)
Y = np.random.normal(0,1,5000)

fig, ax = plt.subplots(1,2, figsize=(6,3), dpi=288)

ax[0].scatter(X,Y, s=.01, c='k')
ax[1].scatter(X,Y, s=1, c='k')
plt.show()

Result:

Notice how the larger dots are opaque and filled in, whilst the smaller ones seem transparent, and have a white facecolor. How do I get the smaller ones to be filled in as well?

Answer 1

If you want the size to scale correctly, and print down to the pixel limit, the dpi and figure size need to be adjusted. Then s will behave correctly, starting with the smallest pixel being s=1. You also probably want to change the marker from the default. Try this:

#divide dpi by four, multiply figsize components by four to keep same area
fig, ax = plt.subplots(1,2, figsize=(24,12), dpi=72)

ax[0].scatter(X,Y, s=1, marker=".", c='k')
ax[1].scatter(X,Y, s=100, marker=".", c='k')

This will make the axes labels smaller, however.

Edit: We can also ensure that the s-value is never sub-minimal-pixel size, as pointed out in comments. Here's a function that allows one to play around with these settings using this:

def scat_rand(size=(24,12), scale=72, smin=1, smax=100, sedge=True, min_pix=1):
    X = np.random.normal(0,1,5000)
    Y = np.random.normal(0,1,5000)
    fig, ax = plt.subplots(1,2, figsize=(size), dpi=scale)

    slimit = (min_pix * 72 / fig.dpi) ** 2
    if smin < slimit + .0001:
        smin = slimit
        print(f"smin too small, reset to {slimit}")

    if sedge:
        ax[0].scatter(X,Y, s=smin, c='k')
        ax[1].scatter(X,Y, s=smax, c='k')
    else:
        ax[0].scatter(X,Y, s=smin, c='k', edgecolor='none')
        ax[1].scatter(X,Y, s=smax, c='k', edgecolor='none')
    plt.suptitle(f"Pixel= {size[0] * scale} x {size[1] * scale}", fontsize=14) 
    plt.show()

Here's a little driver if you want to play around with it:

if __name__ == "__main__":
    temp = int(input("Enter size(1-24): "))
    size = (2 * temp, temp)
    scale = int(input("Enter dpi scale (72, 144, 288, 576, 1152): "))
    limit = (72 / scale) ** 2
    smin = float(input(f"Enter smallest point (limit = {limit}): "))
    smax = float(input("Enter largest point: "))
    edge = input("edgecolor (y/n): ")
    if edge == 'y':
        sedge = True
    else: 
        sedge = False
    scat_rand(size, scale, smin, smax, sedge)

See also: Relationship between dpi and figure size