How to get Bokeh to scale scatter plot size according to zoom

For circles, set the radius kwarg instead of the size value. (There similar, glyph-specific values for the other glyph-types).

i.e.:

plot.circle(x=[1,2,3], y=[1,2,3], radius=0.5)

size is always rendered in screen coordinates (pixels), but radius and the related properties are computed in data coordinates and should change in magnitude with zooming.

Here's a good demo by Bryan Van de Ven showing the difference between pixel coordinates (size) and data coordinates (radius) given in this conference talk:

Intro to Data Visualization with Bokeh - Part 2 - Strata Hadoop San Jose 2016

... the point is all of these attributes can be vectorized. We could for instance say size equals you know 2, 4, 6, 8, 10, and now the size is modulated right. So we have one that has size 2 and one that has size 4. Size is usually in pixels, radius is usually in data dimension units. But all the other ones here as well all the colors, all the visual attributes can be vectorized in this way. You can either give them a single value as we've done for instance with the line fill color, or you can give them a vector of values in which case all of the things are different.

So next exercise here you go to this notebook this is that second notebook "02 - plotting" it is to try to create the same example but now set the radius instead of the size and sort of see what's the difference if you set if you set radius instead of size.