scanpy.external.pl.scrublet_score_distribution

scanpy.external.pl.scrublet_score_distribution(adata, scale_hist_obs='log', scale_hist_sim='linear', figsize=(8, 3))

Plot histogram of doublet scores for observed transcriptomes and simulated doublets.

The histogram for simulated doublets is useful for determining the correct doublet score threshold.

Parameters

adata

An annData object resulting from func:~scanpy.external.scrublet.

scale_hist_obs : strstr (default: 'log')

Set y axis scale transformation in matplotlib for the plot of observed transcriptomes (e.g. “linear”, “log”, “symlog”, “logit”)

scale_hist_sim : strstr (default: 'linear')

Set y axis scale transformation in matplotlib for the plot of simulated doublets (e.g. “linear”, “log”, “symlog”, “logit”)

figsize : Tuple[float, float], NoneOptional[Tuple[float, float]] (default: (8, 3))

width, height

See also

scrublet()

Main way of running Scrublet, runs preprocessing, doublet simulation (this function) and calling.

scrublet_simulate_doublets()

Run Scrublet’s doublet simulation separately for advanced usage.