Non cell type markers

[marcovarrone]

It's possible to define non-cell-type markers in the configuration talbe. Those markers will not be used for cell type classification, but their intensity will be used to divide cells into positive or negative for that marker. This is a generalization of the previous implementation, that was specific for Ki67 (proliferation marker).

• The configuration tables must contain a new column called Is_CellType_Marker that can be either TRUE or FALSE.
• The plots will not include proliferating vs not proliferating, but marker+ vs marker-. The old proliferating cells are now Ki67+.
• Neighborhood analyses does not require the --celltype_query_proliferation_status parameter anymore, but requires the the path to the configuration table using the parameter --channel_info_path.
• Neighborhood analyses outputs plots and tables for cells negative for all markers, but also for cells positive for each marker individually. The file names also include the query cell type.

[danieletavernari]

• Handling case of one non-cell type marker in ClassifyCells_Analyses.R
• set args.lymphomoids_to_process=='all' (instead of args.lymphomoids_to_process=='all[0]' - possibly depends on Python version?) in NeighbourhoodAnalyses.py