scGate: Filter single-cell data by cell type

Description

Apply scGate to filter specific cell types in a query dataset

Usage

scGate(
  data,
  model,
  pos.thr = 0.2,
  neg.thr = 0.2,
  assay = NULL,
  slot = "data",
  ncores = 1,
  BPPARAM = NULL,
  seed = 123,
  keep.ranks = FALSE,
  reduction = c("calculate", "pca", "umap", "harmony"),
  min.cells = 30,
  nfeatures = 2000,
  pca.dim = 30,
  param_decay = 0.25,
  maxRank = 1500,
  output.col.name = "is.pure",
  k.param = 30,
  smooth.decay = 0.1,
  smooth.up.only = FALSE,
  genes.blacklist = "default",
  return.CellOntology = TRUE,
  multi.asNA = FALSE,
  additional.signatures = NULL,
  save.levels = FALSE,
  verbose = FALSE,
  progressbar = T
)

Value

A new metadata column is.pure is added to the query Seurat object, indicating which cells passed the scGate filter. The active.ident is also set to this variable.

Arguments

data: Seurat object containing a query data set - filtering will be applied to this object
model: A single scGate model, or a list of scGate models. See Details for this format
pos.thr: Minimum UCell score value for positive signatures
neg.thr: Maximum UCell score value for negative signatures
assay: Seurat assay to use
slot: Data slot in Seurat object to calculate UCell scores
ncores: Number of processors for parallel processing
BPPARAM: A [BiocParallel::bpparam()] object that tells scGate how to parallelize. If provided, it overrides the `ncores` parameter.
seed: Integer seed for random number generator
keep.ranks: Store UCell rankings in Seurat object. This will speed up calculations if the same object is applied again with new signatures.
reduction: Dimensionality reduction to use for knn smoothing. By default, calculates a new reduction based on the given assay; otherwise you may specify a precalculated dimensionality reduction (e.g. in the case of an integrated dataset after batch-effect correction)
min.cells: Minimum number of cells to cluster or define cell types
nfeatures: Number of variable genes for dimensionality reduction
pca.dim: Number of principal components for dimensionality reduction
param_decay: Controls decrease in parameter complexity at each iteration, between 0 and 1. param_decay == 0 gives no decay, increasingly higher param_decay gives increasingly stronger decay
maxRank: Maximum number of genes that UCell will rank per cell
output.col.name: Column name with 'pure/impure' annotation
k.param: Number of nearest neighbors for knn smoothing
smooth.decay: Decay parameter for knn weights: (1-decay)^n
smooth.up.only: If TRUE, only let smoothing increase signature scores
genes.blacklist: Genes blacklisted from variable features. The default loads the list of genes in scGate::genes.blacklist.default; you may deactivate blacklisting by setting genes.blacklist=NULL
return.CellOntology: If TRUE Cell ontology name and id are returned as additional metadata columns when running multiple models.
multi.asNA: How to label cells that are "Pure" for multiple annotations: "Multi" (FALSE) or NA (TRUE)
additional.signatures: A list of additional signatures, not included in the model, to be evaluated (e.g. a cycling signature). The scores for this list of signatures will be returned but not used for filtering.
save.levels: Whether to save in metadata the filtering output for each gating model level
verbose: Verbose output
progressbar: Whether to show a progressbar or not

Details

Models for scGate are data frames where each line is a signature for a given filtering level. A database of models can be downloaded using the function get_scGateDB. You may directly use the models from the database, or edit one of these models to generate your own custom gating model.

Multiple models can also be evaluated at once, by running scGate with a list of models. Gating for each individual model is returned as metadata, with a consensus annotation stored in scGate_multi metadata field. This allows using scGate as a multi-class classifier, where only cells that are "Pure" for a single model are assigned a label, cells that are "Pure" for more than one gating model are labeled as "Multi", all others cells are annotated as NA.

Examples

Run this code

# \donttest{
### Test using a small toy set
data(query.seurat)
# Define basic gating model for B cells
my_scGate_model <- gating_model(name = "Bcell", signature = c("MS4A1")) 
query.seurat <- scGate(query.seurat, model = my_scGate_model, reduction="pca")
table(query.seurat$is.pure)
### Test with larger datasets
library(Seurat)
testing.datasets <- get_testing_data(version = 'hsa.latest')
seurat_object <- testing.datasets[["JerbyArnon"]]
# Download pre-defined models
models <- get_scGateDB()
seurat_object <- scGate(seurat_object, model=models$human$generic$PanBcell)
DimPlot(seurat_object)
seurat_object_filtered <- subset(seurat_object, subset=is.pure=="Pure")

### Run multiple models at once
models <- get_scGateDB()
model.list <- list("Bcell" = models$human$generic$Bcell,
                   "Tcell" = models$human$generic$Tcell)
seurat_object <- scGate(seurat_object, model=model.list)
DimPlot(seurat_object, group.by = "scGate_multi")
# }