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I've observed the same issue. Here is a small example to reproduce it:
# The following code illustrates a bug in the pyplot.subplots function of version 1.3 of matplotlibimportmatplotlib.pyplotasplt# The following works as expectedfig1, axes1=plt.subplots(1, 2, sharex=True)
axes1[0].plot([1,2,3], [4,5,6])
axes1[1].plot([1,2,3], [11, 12, 13])
# The following does not work as expectedfig2, axes2=plt.subplots(1, 3, sharey=True)
axes2[0].plot([1,2,3], [4,5,6])
axes2[1].plot([1,2,3], [11, 12, 13])
plt.show()
As long as all the plots are filled,

subplots(n, m, sharex=True, sharey=True)
works fine.When some plots are left blank, though, the shared axis scales according to the empty plots, making it impossible to see the filled ones.

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