White lines in matplotlib's pcolor

The comments have a good solution that utilizes imshow. When imshow is not appropriate for the input data (e.g. it is not uniformly spaced) this generally solves this problem,

pcol = pl.pcolormesh(x,y,z,cmap="Blues",linewidth=0,)
pcol.set_edgecolor('face')

If that approach does not reduce the lines sufficiently, you can also try this:

pl.pcolormesh(x,y,z,cmap="Blues",linewidth=0,rasterized=True)

In addition to reducing the lines between squares this approach also tends to reduce file size a bit, which is sometimes useful. In this case you may want to tune the dpi setting when saving (e.g. pl.savefig("heatmap.pdf", dpi=300)) until you get something that is satisfactory.

The accepted answer didn't work very well for me. I seemed to have gotten closer by using antialiased=True, in addition to linewidth=0. This was with matplotlib version 3.0.2. Note the middle plot corresponds to the best version.

fig, axes = plt.subplots(1,3, figsize=(15,5))
axes[0].pcolormesh(XX, YY, ZZ_r, zorder=-1, norm=norm, cmap='magma', alpha=0.5, antialiased=True)
axes[1].pcolormesh(XX, YY, ZZ_r, zorder=-1, norm=norm, cmap='magma', alpha=0.5, antialiased=True, linewidth=0.0)
axes[2].pcolormesh(XX, YY, ZZ_r, zorder=-1, norm=norm, cmap='magma', alpha=0.5, antialiased=False, linewidth=0.0)

I had this problem, using rasterized=True solved it (on matplotlib version 3.1.0).