For an application I am developing, I need to callax.scatter then change the colors of the points after the fact. However, if the input x/y values contain NaN values, then setting the colors after the fact doesn't work properly. The following example:

importmatplotlibmatplotlib.use('Agg')importnumpyasnpimportmatplotlib.pyplotaspltfig=plt.figure()ax=fig.add_subplot(1,1,1,aspect='auto')x=np.array([1,2,3])y=np.array([2,np.nan,4])c=np.array([3,4,5])s=ax.scatter(x,y,c=c,vmin=3,vmax=5,s=320,zorder=1,edgecolor='none')s=ax.scatter(x,y,s=160,zorder=2,edgecolor='none')s.set_array(c)s.set_clim(3,5)s=ax.scatter([], [],s=40,zorder=3,edgecolor='none')s.set_offsets(np.vstack([x,y]).transpose())s.set_array(c)s.set_clim(3,5)fig.savefig('test.png')

produces the following output:

The top right point should be all yellow. However it isn't, because in thescatter call, invalid values are removed, so when I try and set the colors withset_array, the color values are offset from the x/y values. In the final case, things work since the 'bad' values are masked from neither the offsets nor the colors.

Is there a way to achieve something along the lines of the middle example (setting the colors after the fact)