misalignment between grid cells and color mesh used to highlight them (in Matplotlib)

Question

I am using the following code to to generate this heat map:

dim = np.arange(1, 32, 1)

fig, ax = plt.subplots(figsize=(7,9))
heatmap = ax.imshow(h, aspect=1, cmap=plt.cm.get_cmap('Blues', 5), clim=[0,100])
ax.set_ylabel("Days", fontsize=15)
ax.set_xlabel("Months", fontsize=15)
ax.set_title("Percentage of records per day", fontsize=18)
ax.set_yticks(range(0,31))
ax.set_yticklabels(dim, ha='center', minor=False)
ax.set_xticks(range(0,13,1))
ax.set_xticklabels(ylabel[7:],rotation=45, ha='right')
ax.grid(which = 'minor', color = 'w')
ax.set_facecolor('gray')
ax.xaxis.set_minor_locator(MultipleLocator(.5))
ax.yaxis.set_minor_locator(MultipleLocator(.5))
cbaxes = fig.add_axes([.8, .35, .04, .3])
cbar = fig.colorbar(heatmap, ticks = [0, 20, 40, 60, 80 ,100], label =  'Percentage', cax = cbaxes)
fig.show()

I would like to highlight all of the cells with a value greater or equal to 60. I tried adding this to my code:

highlight = (h> 60)
highlight = np.ma.masked_less(highlight, 1)
ax.pcolormesh(highlight, facecolor = 'None')

and got this:

I am almost there but the cells and the mesh are misaligned. How could I fix this?

Answer 1

The cells in a heatmap are centered on integers, this means for example that the cell with index 0,0 is in fact -0.5 to 0.5 on both axes. You have to subtract 0.5 to the coordinates of your highlights.