Making the marker size as small as possible with matplotlib.pyplot

Question

My program can generate up to 2000000 points within 5 seconds, so I don't have a problem with speed. Right now I am using matplotlib.pyplot.scatter to scatter all my points on my graph. For s=1, it gives me small circles, but not small enough, because it does not show the intricate patterns. When I use s=0.1, it gives me this weird marker shape:

Which makes the marker larger despite me making the size smaller. I have searched all over the internet including stack overflow, but they do not tell how to minimize the size further. Unfortunately, I have to show all the points, and cannot just show a random sample of them.

I have come to the conclusion that matplotlib is made for a small sample of points and not meant for plotting millions of points. However, if it is possible to make the size smaller please let me know.

Anyway, for my points, I have all the x values in order in one array, and all the y values in order in another array. Could someone suggest a graphing package in python I could use to graph all the points in a way that the size would be very small since when I plot the points now it just becomes one big block of color instead of intricate designs forming in the shape as they should be.

Thanks for any help in advance!

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EDIT: My code that I am using to scatter the points is:

plt.savefig(rootDir+"b"+str(Nvertices)+"_"+str(xscale)+"_"+str(yscale)+"_"+str(phi)+"_"+str(psi)+"_"+CurrentRun+"_color.png", dpi =600)

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EDIT: I got my answer, I added linewidths = 0 and that significantly reduced the size of the points, giving me what I needed.

Hilbert

Your question doesn't show any code, so it is hard to guess which parameters you're using. You might try to remove the boundary line (lw=0 if you're using plt.scatter) – Shovelnose

Answer 1

Perhaps you can try making the linewidths as 0 i.e., the line width of the marker edges. Notice the difference in the two plots below

fig, ax = plt.subplots(figsize=(6, 4))
plt.scatter(np.random.rand(100000), np.random.rand(100000), s=0.1)

fig, ax = plt.subplots(figsize=(6, 4))
plt.scatter(np.random.rand(100000), np.random.rand(100000), s=0.1, linewidths=0)

Dodecahedron

Thank you this helped so much! This definitely improved my program. – Hilbert

If you're using plt.plot, the solution is to use markeredgecolor='none' as mentioned by @Shovelnose in the comments of this question. – Childbearing

If you are editing the Line2D object after it is generated then use child.set_markeredgewidth(0) – Ylla

Answer 2

you can set the marker to a single pixel using marker=',' in your call to scatter.

See the markers documentation here

Hematology