scatter plot with single pixel marker in matplotlib

The problem

I fear that the bugfix discussed at matplotlib git repository that you're citing is only valid for plt.plot() and not for plt.scatter()

import matplotlib.pyplot as plt

fig = plt.figure(figsize=(4,2))
ax = fig.add_subplot(121)
ax2 = fig.add_subplot(122, sharex=ax, sharey=ax)
ax.plot([1, 2],[0.4,0.4],color='black',marker=',',lw=0, linestyle="")
ax.set_title("ax.plot")
ax2.scatter([1,2],[0.4,0.4],color='black',marker=',',lw=0, s=1)
ax2.set_title("ax.scatter")
ax.set_xlim(0,8)
ax.set_ylim(0,1)
fig.tight_layout()
print fig.dpi #prints 80 in my case
fig.savefig('plot.png', dpi=fig.dpi)

The solution: Setting the markersize

The solution is to use a usual "o" or "s" marker, but set the markersize to be exactly one pixel. Since the markersize is given in points, one would need to use the figure dpi to calculate the size of one pixel in points. This is 72./fig.dpi.

• For aplot`, the markersize is directly

  ax.plot(..., marker="o", ms=72./fig.dpi)
  

• For a scatter the markersize is given through the s argument, which is in square points,

  ax.scatter(..., marker='o', s=(72./fig.dpi)**2)
  

Complete example:

import matplotlib.pyplot as plt

fig = plt.figure(figsize=(4,2))
ax = fig.add_subplot(121)
ax2 = fig.add_subplot(122, sharex=ax, sharey=ax)
ax.plot([1, 2],[0.4,0.4], marker='o',ms=72./fig.dpi, mew=0, 
        color='black', linestyle="", lw=0)
ax.set_title("ax.plot")
ax2.scatter([1,2],[0.4,0.4],color='black', marker='o', lw=0, s=(72./fig.dpi)**2)
ax2.set_title("ax.scatter")
ax.set_xlim(0,8)
ax.set_ylim(0,1)
fig.tight_layout()
fig.savefig('plot.png', dpi=fig.dpi)

For anyone still trying to figure this out, the solution I found was to specify the s argument in plt.scatter.

The s argument refers to the area of the point you are plotting.

It doesn't seem to be quite perfect, since s=1 seems to cover about 4 pixels of my screen, but this definitely makes them smaller than anything else I've been able to find.

https://matplotlib.org/devdocs/api/_as_gen/matplotlib.pyplot.scatter.html

s : scalar or array_like, shape (n, ), optional
size in points^2. Default is rcParams['lines.markersize'] ** 2.