how to merge many points of a scatterplot made with matplotlib

howto.md

Approach A

1. Export the plot as SVG

   plt.savefig("plot.svg")

2. Open plot.svg with an editor and include in the definitions the following:

<defs>
   <filter id="shadow">
      <feOffset dx="0" dy="0"/>
      <feMerge>
        <feMergeNode/>
        <feMergeNode in="SourceGraphic"/>
      </feMerge>
    </filter>
  </defs>

3. Then, for each group of point replace:

<g clip-path="url(#pde120285b9)">

to this:

<g filter="url(#shadow)" clip-path="url(#pde120285b9)">    

The clip-path may vary.

4. Finally, use rsvg-convert to convert svg to pdf:

rsvg-convert -d 600 -p 600 -f pdf -o output.pdf input.svg

where 600x600 represents the dpi in each axis.

Approach B

1. For each plot that you want to rasterize use:

plt.plot(..., rasterized=True)

2. Save setting dpi:

plt.savefig('dots.pdf', dpi=600) 

Differences of the approaches

Using these two approaches in a plot with more than 100k+ points:

1.2M original_file.pdf
160K approach_a.pdf
272K approach_b.pdf

Verdict

Although the first approach (in this test) results in a smaller file, it's quite easier to use the Approach B than Approach A. Thus, Approach B will be.