Annotate single cells using scmap.

Usage

RunScmap(
  srt_query,
  srt_ref,
  ref_group = NULL,
  query_assay = "RNA",
  ref_assay = "RNA",
  method = "scmapCluster",
  nfeatures = 500,
  threshold = 0.5,
  k = 10
)

Arguments

srt_query: An object of class Seurat to be annotated with cell types.
srt_ref: An object of class Seurat storing the reference cells.
ref_group: A character vector specifying the column name in the `srt_ref` metadata that represents the cell grouping.
query_assay: A character vector specifying the assay to be used for the query data. Defaults to the default assay of the `srt_query` object.
ref_assay: A character vector specifying the assay to be used for the reference data. Defaults to the default assay of the `srt_ref` object.
method: The method to be used for scmap analysis. Can be any of "scmapCluster" or "scmapCell". The default value is "scmapCluster".
nfeatures: The number of top features to be selected. The default value is 500.
threshold: The threshold value on similarity to determine if a cell is assigned to a cluster. This should be a value between 0 and 1. The default value is 0.5.
k: Number of clusters per group for k-means clustering when method is "scmapCell".

Examples

data("panc8_sub")
# Simply convert genes from human to mouse and preprocess the data
genenames <- make.unique(capitalize(rownames(panc8_sub), force_tolower = TRUE))
#> Error in capitalize(rownames(panc8_sub), force_tolower = TRUE): could not find function "capitalize"
panc8_sub <- RenameFeatures(panc8_sub, newnames = genenames)
#> Error: object 'genenames' not found
panc8_sub <- check_srtMerge(panc8_sub, batch = "tech")[["srtMerge"]]
#> Warning: Failed to check Seurat version compatibility: 'list' object cannot be coerced to type 'double'
#> [2025-09-08 16:17:13.510224] Spliting srtMerge into srtList by column tech... ...
#> [2025-09-08 16:17:13.690797] Checking srtList... ...
#> Warning: Failed to check Seurat version compatibility: 'list' object cannot be coerced to type 'double'
#> Warning: The following arguments are not used: drop
#> Warning: The following arguments are not used: drop
#> Error in as.vector(data): no method for coercing this S4 class to a vector

# Annotation
data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
#> [2025-09-08 16:17:14.912244] Start Standard_SCP
#> [2025-09-08 16:17:14.912441] Checking srtList... ...
#> Warning: Failed to check Seurat version compatibility: 'list' object cannot be coerced to type 'double'
#> Warning: The following arguments are not used: drop
#> Warning: The following arguments are not used: drop
#> Error in as.vector(data): no method for coercing this S4 class to a vector
pancreas_sub <- RunScmap(
  srt_query = pancreas_sub, srt_ref = panc8_sub,
  ref_group = "celltype", method = "scmapCluster"
)
#> Error in check_R("scmap"): could not find function "check_R"
CellDimPlot(pancreas_sub, group.by = "scmap_annotation")
#> Error in CellDimPlot(pancreas_sub, group.by = "scmap_annotation"): scmap_annotation is not in the meta.data of srt object.

pancreas_sub <- RunScmap(
  srt_query = pancreas_sub, srt_ref = panc8_sub,
  ref_group = "celltype", method = "scmapCell"
)
#> Error in check_R("scmap"): could not find function "check_R"
CellDimPlot(pancreas_sub, group.by = "scmap_annotation")
#> Error in CellDimPlot(pancreas_sub, group.by = "scmap_annotation"): scmap_annotation is not in the meta.data of srt object.