Bering.tools.cell_annotation

Bering.tools.cell_annotation(bg, min_transcripts=50, min_dominant_nodes=30, min_dominant_ratio=0.6)[source]

Annotate segmented cells based on ensemble strategy. A cell is considered as a qualified cell if it satisfies all of the following criteria: - Number of transcripts > min_transcripts; - Number of dominant nodes > min_dominant_nodes; - Ratio of dominant nodes > min_dominant_ratio.

Other than that, the cell is not considered as a segmented cell and transcipts within this cell are assigned to the background.

Parameters:

bg (BrGraph) – Bering graph object
min_transcripts (int) – Minimum number of transcripts for a cell to be considered
min_dominant_nodes (int) – Minimum number of dominant nodes for a cell to be considered
min_dominant_ratio (float) – Minimum ratio of dominant nodes for a cell to be considered