Pytometry and dot plot function of scanpy

[Paolo]

Hello!
I'm using Pytometry to analyze my Flow Cytometry data. I've already used Scanpy for the analysis of scRNA-seq data.
I want to use the scanpy dot plot function on the anndata created with the FCS files, but something is wrong with the size (so the frequency) of dots in the dot plot. In my panel there are two markers that are mutually exclusive: indeed, when the expression of one is red the other one is white. The problem is related to the size of the dots of the negative population because it is as big as the positive one.
Is there a way to fix this in my code?

Thanks for the help!

[Maren Büttner]

Hi @pmarzano97

thanks for using Pytometry.
In flow data, "not expressed" does not necessarily mean that you do not have any signal (as in transcriptomics). The dotplot function in scanpy uses the expression_cutoff (defaults to 0.0) to determine where a marker is expressed - by increasing the expression cutoff, you will get the expected picture, I assume.