Auto-annotate cell types (multi-backend wrapper)

Usage

auto_annotate(
  obj,
  species = c("mouse", "human"),
  assay = "RNA",
  prefer = c("sctype", "marker_score", "singleR", "label_transfer"),
  level = c("cluster", "cell"),
  marker_score_level = c("cluster", "cell"),
  custom_signatures = NULL,
  ref_seurat = NULL,
  ref_label_col = NULL,
  unknown_min_genes = 2,
  unknown_min_margin = 0.01,
  unknown_min_top = 0.01,
  organ = NULL,
  sctype_db_path = NULL,
  marker_method = c("module_score", "findmarkers"),
  panglao_file = system.file("extdata", "PanglaoDB_markers_27_Mar_2020.tsv", package =
    utils::packageName()),
  panglao_tissue = NULL,
  panglao_ui_max = 0.2,
  panglao_canonical_only = TRUE,
  fm_top_n = 50,
  fm_padj_max = 0.05,
  overlap_mode = c("count", "jaccard")
)

Arguments

obj: Seurat object.
species: Character, "mouse" or "human".
assay: Assay to use (default "RNA").
prefer: Optional character; preferred backend(s) to try first.
level: "cell" or "cluster".
marker_score_level: Level for marker_score ("cell"/"cluster").
custom_signatures: Optional list/data.frame of custom markers.
ref_seurat: Optional Seurat reference object (label transfer).
ref_label_col: Column in ref_seurat@meta.data with labels.
unknown_min_genes: Integer; minimum genes to avoid "unknown".
unknown_min_margin: Numeric; min score margin to call a label.
unknown_min_top: Integer; min top markers expressed to call a label.
organ: Optional organ/tissue context string.
sctype_db_path: Optional path to ScType flat DB (xlsx).
marker_method: Marker backend when using marker-based annotation.
panglao_file: Optional PanglaoDB CSV/XLSX file path.
panglao_tissue: Optional tissue filter for PanglaoDB.
panglao_ui_max: Integer; cap markers per type to avoid overplot.
panglao_canonical_only: Logical; keep only canonical markers.
fm_top_n: Integer; FindMarkers top N to keep per cluster.
fm_padj_max: Numeric; padj cutoff for FindMarkers filtering.
overlap_mode: How to combine/overlap multiple marker sources.

Value

Seurat object with annotation columns added.