White lines in matplotlib’s pcolor

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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.

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