pace.plot_proximity

pace.plot_proximity(fit, counts, genes, focal, neighbour, ax=None, radius=30.0, breaks=(0, 2, 4, 6, 8, inf))

A gene’s raw counts against how many of a neighbour type a cell has.

One panel per gene, drawn as R draws it: boxplots over bins of the NEIGHBOUR COUNT within radius, with the bin mean as a filled point. The mean is what carries the trend here – these counts are zero-inflated, so the box median sits at zero in most bins and says nothing.

The fitted kernel is the other thing one could bin on, but it is centred within image, so its axis runs negative and means nothing on its own.