scoloc: SColoc module

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

SColoc module

Description

SColoc module

Usage

scoloc(
  celltrek_inp,
  col_cell = "cell_names",
  use_method = c("KL", "DT", "KD")[2],
  h = celltrek_inp@images[[1]]@scale.factors$spot_dis,
  n = 25,
  boot_n = 20,
  ...
)

Arguments

celltrek_inp	CellTrek input
col_cell	Column name of cell type, cell type names must be syntactically valid
use_method	Use density-based Kullback Leibler divergence or Delaunay Triangulation network
h	Bandwidths for x and y directions, for KL, more details in kde2d function in MASS package
n	Number of grid points in each directions, for KL, more details in kde2d function in MASS package
...	See in boot_mst

Value

A list of 1.Bootstrap distance; 2.MST consensus matrix

Examples

cell_scoloc <- scoloc(celltrek_inp, col_cell='cell_names', use_method='KL', h=140, n=25)

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