traint: Co-embedding ST and SC data using Seurat transfer anchors

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

Co-embedding ST and SC data using Seurat transfer anchors

Description

Co-embedding ST and SC data using Seurat transfer anchors

Usage

traint(
  st_data,
  sc_data,
  st_assay = "Spatial",
  sc_assay = "scint",
  norm = "LogNormalize",
  nfeatures = 2000,
  cell_names = "cell_names",
  coord_xy = c("imagerow", "imagecol"),
  gene_kept = NULL,
  ...
)

Arguments

st_data	Seurat ST data object
sc_data	Seurat SC data object
st_assay	ST assay
sc_assay	SC assay
norm	normalization method: LogNormalize/SCTransform
nfeatures	number of features for integration
cell_names	cell cluster/type column name in SC meta data
coord_xy	coordinates column names in ST images slot
gene_kept	selected genes to be kept during integration

Value

Seurat object of SC-ST co-embedding

Examples

st_sc_traint <- traint(st_data=brain_st, sc_data=brain_sc, st_assay='Spatial', sc_assay='scint', nfeatures=2000, cell_names='cell_names', coord_xy=c('imagerow', 'imagecol'), gene_kept=NULL)

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