Run CellTypist cell type annotation

CellTypist is an automated cell type annotation tool for scRNA-seq datasets based on logistic regression classifiers. This function runs CellTypist annotation on a Seurat object or AnnData object.

Usage

RunCellTypist(
  srt = NULL,
  adata = NULL,
  assay = "RNA",
  layer = "data",
  model = "Immune_All_Low.pkl",
  mode = "best match",
  p_thres = 0.5,
  majority_voting = FALSE,
  over_clustering = NULL,
  min_prop = 0,
  use_GPU = FALSE,
  insert_labels = TRUE,
  insert_conf = TRUE,
  insert_conf_by = "predicted_labels",
  insert_prob = FALSE,
  insert_decision = FALSE,
  prefix = "celltypist_",
  return_seurat = !is.null(srt),
  verbose = TRUE
)

Arguments

srt

A Seurat object. Default is NULL. If provided, adata will be ignored.

adata

An anndata object. Default is NULL.

assay

Assay to convert in the anndata object.

layer

Layer name for assay in the Seurat object.

model

Model name or path. Default is "Immune_All_Low.pkl". Supports three formats:

Model name (e.g., "Immune_All_Low.pkl"): automatically searched in ~/.celltypist/data/models/
Full path (contains /): use the provided path directly
NULL: use default model

mode

Prediction mode: "best match" or "prob match". Default is "best match".

p_thres

Probability threshold for "prob match" mode. Default is 0.5.

majority_voting

Whether to use majority voting. Default is FALSE.

over_clustering

Over-clustering result. Can be:

String: column name in Seurat metadata or AnnData obs
Vector: over-clustering labels
NULL: use heuristic over-clustering

min_prop

Minimum proportion for majority voting. Default is 0.

use_GPU

Whether to use GPU for over-clustering. Default is FALSE.

insert_labels

Whether to insert predicted labels. Default is TRUE.

insert_conf

Whether to insert confidence scores. Default is TRUE.

insert_conf_by

Which prediction type to base confidence on. Default is "predicted_labels".

insert_prob

Whether to insert probability matrix. Default is FALSE.

insert_decision

Whether to insert decision matrix. Default is FALSE.

prefix

Prefix for inserted columns. Default is "celltypist_".

return_seurat

Whether to return a Seurat object instead of an anndata object. Default is TRUE.

verbose

Whether to print the message. Default is TRUE.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunCellTypist(
  pancreas_sub,
  model = "Developing_Mouse_Brain.pkl"
)
CellDimPlot(
  pancreas_sub,
  group.by = "celltypist_predicted_labels",
  legend.position = "none"
)

# Use prob match mode
pancreas_sub <- RunCellTypist(
  pancreas_sub,
  model = "Developing_Mouse_Brain.pkl",
  mode = "prob match",
  p_thres = 0.5
)

# Use majority voting
pancreas_sub <- RunCellTypist(
  pancreas_sub,
  model = "Developing_Mouse_Brain.pkl",
  majority_voting = TRUE
)
} # }

Usage

Arguments

See also

Examples