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Get available CellTypist models

Source: R/RunCellTypist.R
CellTypistModels.Rd

Unified CellTypist model management interface. Use it to list available models, download models, inspect model metadata, extract model markers, subset models, convert models, or delete local models.

Usage

CellTypistModels(
  action = c("list", "download", "info", "markers", "subset", "convert", "delete"),
  on_the_fly = FALSE,
  model = NULL,
  force_update = FALSE,
  cell_type = NULL,
  top_n = 10,
  only_positive = TRUE,
  keep_cell_types = NULL,
  exclude_cell_types = NULL,
  output_model_path = NULL,
  map_file = NULL,
  sep = ",",
  convert_from = NULL,
  convert_to = NULL,
  unique_only = TRUE,
  collapse = c("average", "random"),
  random_state = 0,
  verbose = TRUE
)

Arguments

action

Action to perform. One of "list", "download", "info", "markers", "subset", "convert", or "delete".

on_the_fly

If TRUE, only show downloaded models. If FALSE, show all available models (fetch list from server). Used when action = "list". Default is FALSE.

model

Model name(s) used for actions other than "list".

force_update

Whether to refresh the model index before downloading. Used when action = "download".

cell_type

Cell type used when action = "markers".

top_n

Number of markers to extract when action = "markers".

only_positive

Whether to return only positive markers.

keep_cell_types

Cell types retained when action = "subset".

exclude_cell_types

Cell types removed when action = "subset".

output_model_path

Optional output path used by "subset" or "convert". If NULL, the original model file will be overwritten.

map_file

Optional two-column gene mapping file used by action = "convert".

sep

Delimiter used by map_file.

convert_from, convert_to

Column indices used by map_file.

unique_only

Whether to use only one-to-one mappings in action = "convert".

collapse

How to collapse one-to-many mappings in action = "convert".

random_state

Random seed used when collapse = "random".

verbose

Whether to print the message. Default is TRUE.

Value

Depends on action: a data frame, a summary list, or a character vector.

See also

RunCellTypist, TrainCellTypist

Examples

if (FALSE) { # \dontrun{
# Get available models
models <- CellTypistModels()
print(models)

# Show downloaded models only
local_models <- CellTypistModels(on_the_fly = TRUE)

# Download a model
CellTypistModels(
  action = "download",
  model = "Immune_All_Low.pkl"
)

# Inspect a model
CellTypistModels(
  action = "info",
  model = "Immune_All_Low.pkl"
)

# Extract top markers for a cell type
CellTypistModels(
  action = "markers",
  model = "Immune_All_Low.pkl",
  cell_type = "B cells",
  top_n = 20
)
} # }