Version Compatibility

Reference examples tested with: FlowSOM 2.10+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Clustering and Phenotyping

"Cluster my cytometry data to find cell types" → Discover cell populations in high-dimensional flow/mass cytometry data using unsupervised clustering without predefined gates.

• R: FlowSOM::FlowSOM() for self-organizing map clustering
• R: CATALYST::cluster() with Phenograph or FlowSOM

FlowSOM Clustering

Goal: Cluster cytometry events into cell populations using self-organizing maps.