Hello Bryan.

Thank you for taking the time to help me.

My apologies for being unclear, but I am completely new to this and got confused by the many levels of packaging.

I understand now that sample.plot_scatter a composite function that is calling bokeh and does not support axis rescaling, so let me rephrase the question in a way that you hopefully can answer by explaining what I am trying to do.

The flow cytometer simultaneously measures fluorescence in multiple channels and generates an array with the channels as columns and values for each data point as rows. The R plot above shows the data of 2 chanels plotted against each other on a logarithmic scale.

I want to do that in python with bokeh, so the question amounts to:

“How to I make a 2D scatter plot from a matrix or data frame where the axes are on a log scale”.

The coloring by density is not really mandatory, but would be nice.