RunScmap: Annotate single cells using scmap.

In zh542370159/SCP: Single Cell Pipeline

Annotate single cells using scmap.

Description

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))
panc8_sub <- RenameFeatures(panc8_sub, newnames = genenames)
panc8_sub <- check_srtMerge(panc8_sub, batch = "tech")[["srtMerge"]]

# Annotation
data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
pancreas_sub <- RunScmap(
  srt_query = pancreas_sub, srt_ref = panc8_sub,
  ref_group = "celltype", method = "scmapCluster"
)
CellDimPlot(pancreas_sub, group.by = "scmap_annotation")

pancreas_sub <- RunScmap(
  srt_query = pancreas_sub, srt_ref = panc8_sub,
  ref_group = "celltype", method = "scmapCell"
)
CellDimPlot(pancreas_sub, group.by = "scmap_annotation")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.