plot shapes of filtered out cells

[lopollar]

In order to visualize the cells that are filtered out, we will need to keep them. I propose following:

• [x] Check if we can save an extra column in the shapes to save when filtered out
• [x] if we are filtering cells out, add them to filtered and make it possible to plot these in the pot_shapes
• [x] plot these cells black/gray and make it a parameter

[lopollar]

We can't save a column in the shapes object, so object for every different added layer of filtered cells. Added the plot_filtered to the code!