pyplot.scatter reduce marker size

Question

Here is an example of a scatter plot with high 2D point density, just for illustration.

How can I reduce the size of the markers to better distinguish the individual points? The size of the plot should remain as it is.

import numpy as np
import matplotlib.pyplot as plt
from sklearn import preprocessing
from matplotlib import cm

np.random.seed(10)

n=3000

x = np.arange(n)
z = np.sin(x/n)
y = np.random.randint(0, 100, size=(n))

colvals = preprocessing.minmax_scale(z)

plt.scatter(x, y, color=cm.rainbow(colvals), marker='.')
plt.xlabel('x')
plt.ylabel('y')

plt.show()

@tdy I am wrong, what I said. That is the solution. Thank you very much. You can write this as an answer and I will mark it as solved. It seems that s has no lower boundary? — len, Commented Mar 18, 2022 at 22:22
No problem. Any float is valid (even negative values will only give a warning), so the practical lower bound is just whatever is perceptible to the eye for a given figure. — tdy, Commented Mar 18, 2022 at 22:58

tdy · Accepted Answer · 2022-03-18 23:59:31Z

5

plt.scatter has a parameter s for controlling the marker size.

s can either be a single float that applies to all points, e.g. all size 5:
```
s = 5
plt.scatter(x, y, color=cm.viridis(colvals), marker='.', s=s)
```
Or s can be an array of sizes that maps to every point, e.g. size 5 when z > 0.5 and size 30 otherwise:
```
s = np.where(z > 0.5, 5, 30)
plt.scatter(x, y, color=cm.viridis(colvals), marker='.', s=s)
```

Note that to match the size of scatter and plot markers, the plot marker's markersize should be the square root of the scatter marker's s:

s = 900

plt.scatter(-1, 0, s=s, color='tab:orange')
plt.plot(1, 0, 'o', markersize=s ** 0.5)

edited Mar 18, 2022 at 23:59

answered Mar 18, 2022 at 22:51

tdy

41.6k38 gold badges118 silver badges116 bronze badges

Side note: I swapped out rainbow for viridis since the rainbow colormap should be avoided when possible.
– tdy
Commented Mar 19, 2022 at 0:02
1

Thanks for the link to the interesting paper, many researchers still use rainbow or monochrome color maps with increasing brightness.
– len
Commented Mar 21, 2022 at 7:48

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