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Manually readjust Scrublet doublet call thresholds

call_doublets_manual.Rd

Updates doublet calls and associated summary statistics in a ScrubletRes object using a user-supplied threshold. Intended for use after visual inspection of the score histograms via plot.ScrubletRes().

Usage

call_doublets_manual(
  scrublet_res,
  threshold,
  for_sample = NULL,
  .verbose = TRUE
)

Arguments

scrublet_res

A ScrubletRes object.

threshold

Numeric in [0, 1]. The new threshold to apply.

for_sample

Optional character. For grouped results, the name of the group to update. Defaults to the first group if NULL. Ignored for ungrouped results.

.verbose

Logical. If TRUE, prints updated rate summaries to the console.

Value

The ScrubletRes object with updated predicted_doublets, z_scores, threshold, detected_doublet_rate, detectable_doublet_fraction, and overall_doublet_rate.

Examples

# move the automatic threshold after eyeballing the histograms
sc <- demo_single_cells(prepped = FALSE)
res <- scrublet_sc(
  sc,
  scrublet_params = params_scrublet(
    pca = list(no_pcs = 10L),
    hvg = list(min_gene_var_pctl = 0.0),
    n_bins = 20L
  ),
  .verbose = FALSE
)
call_doublets_manual(res, threshold = 0.3, .verbose = FALSE)
#> ScrubletRes: 500 cells, 5 doublets (1.0%)
#>   Threshold:              0.3000
#>   Detected doublet rate:  1.0%
#>   Detectable fraction:    85.3%
#>   Overall doublet rate:   1.2%
#>   Simulated doublets:     750

unlink(sc@dir_data, recursive = TRUE, force = TRUE)