celltrek_from_dist: CellTrek from a pre-computed SC-ST distance matrix

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

CellTrek from a pre-computed SC-ST distance matrix

Description

CellTrek from a pre-computed SC-ST distance matrix

Usage

celltrek_from_dist(
  dist_mat,
  coord_df,
  dist_cut,
  top_spot = 10,
  spot_n = 10,
  repel_r = 5,
  repel_iter = 10,
  sc_data,
  sc_assay = "RNA",
  st_data = NULL
)

Arguments

dist_mat	Distance matrix of sc-st (sc in rows and st in columns)
coord_df	Coordinates data frame of st (must contain two columns as coord_x, coord_y and rownames as barcodes)
dist_cut	Distance cutoff
top_spot	Maximum number of spots that one cell can be charted
spot_n	Maximum number of cells that one spot can contain
repel_r	Repelling radius
repel_iter	Repelling iterations
sc_data	SC data
sc_assay	SC assay
st_data	ST data, optional

Value

A list of 1.Seurat object

Examples

celltrek_res <- celltrek_from_dist(dist_mat, coord_df, dist_cut, top_spot=10, spot_n=10, r=NULL, sc_data, sc_assay='RNA')

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