run_kdist: Run K-distance with CellTrek(Seurat) object and add a...

In navinlabcode/CellTrek: Spatial Charting of Single Cell Transcriptomes in Tissues

Run K-distance with CellTrek(Seurat) object and add a metadata column

Description

Run K-distance with CellTrek(Seurat) object and add a metadata column

Usage

run_kdist(
  celltrek_inp,
  grp_col = "cell_type",
  ref = NULL,
  ref_type = "all",
  que = NULL,
  k = 10,
  new_name = "kdist",
  keep_nn = F
)

Arguments

celltrek_inp	SChart seurat input
grp_col	Column name in meta data for reference and query groups
ref	Reference groups
ref_type	'all' or 'each'
que	Query groups
k	The number of nearest neighbors
new_name	New name for kdist
keep_nn	Keep Nearest Neighboor id matrix?

Value

SChart seurat output

Examples

celltrek_test <- run_kdist(celltrek_inp=celltrek_inp, grp_col='cell_type', ref=c('A', 'B'), ref_type='each', que=unique(test_df$cell_names), k=10)

navinlabcode/CellTrek documentation built on April 15, 2022, 8:04 a.m.