Benchmark single-cell integration methods

Run one or more RunIntegration() methods on the same input, score each latent embedding with scIB-style batch-correction and bio-conservation metrics (scaled iLISI/cLISI, ASW, graph connectivity, ARI/NMI), and store the tables in srt@tools$IntegrationBenchmark. The object itself is returned so later plotting can reuse the embeddings and per-cell LISI scores.

Usage

RunIntegrationBenchmark(
  srt,
  batch,
  celltype = NULL,
  methods = c("Uncorrected", "Harmony"),
  linear_reduction = "pca",
  nHVF = 2000,
  linear_reduction_dims = 50,
  linear_reduction_dims_use = NULL,
  nonlinear_reduction = "umap",
  perplexity = 30,
  k_graph = 15,
  bio_weight = 0.6,
  batch_weight = 0.4,
  skip_failed = TRUE,
  tool_name = "IntegrationBenchmark",
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object containing a batch column.

batch

Metadata column used as the technical batch.

celltype

Optional metadata column used as biological labels.

methods

Integration methods passed to RunIntegration().

perplexity

Neighborhood size for RunLISI().

k_graph

Neighbor size for graph connectivity.

bio_weight, batch_weight

Weights used for the overall score. Defaults follow scIB (0.6 bio conservation, 0.4 batch correction).

skip_failed

Whether a failed method is recorded and skipped.

tool_name

Name of the srt@tools entry used to store the tables.

verbose

Whether to print the message. Default is TRUE.

...

The message to print.

Value

The input Seurat object with integration reductions, per-cell LISI columns, and srt@tools[[tool_name]] containing summary, metrics, and runs. Print the tables with thisplot::print_colored_table().

See also

IntegrationBenchmarkPlot, RunIntegration, RunLISI

Examples

if (FALSE) { # \dontrun{
data(panc8_sub)
panc8_sub <- RunIntegrationBenchmark(
  panc8_sub,
  batch = "tech",
  celltype = "celltype",
  methods = c("Uncorrected", "Harmony"),
  nHVF = 500,
  linear_reduction_dims = 20,
  linear_reduction_dims_use = 1:10,
  perplexity = 10
)
thisplot::print_colored_table(
  panc8_sub@tools$IntegrationBenchmark$summary,
  by = "row",
  palette = "Chinese"
)
thisplot::print_colored_table(
  panc8_sub@tools$IntegrationBenchmark$metrics,
  by = "col",
  palette = "Paired"
)
IntegrationBenchmarkPlot(panc8_sub)
IntegrationBenchmarkPlot(panc8_sub, plot_type = "box")
} # }