This function generates cell locations for all regions.
Usage
cell.loc.fc(
N,
win,
cell.prop,
cell.inh.attr.input = NULL,
same.dis.cutoff = 0,
even.distribution.coef = 0,
grid.size.small = 19,
grid.size.large = 45,
seed
)Arguments
- N
No. of cells to generate.
- win
Spatial window within which cells will be generated.
- cell.prop
Proportion of cell in each cell type to generated for each region.
- cell.inh.attr.input
(Default=NULL). A matrix providing cell-cell location attraction and inhibition parameters. Example input is like: cell.inh.attr.input= cbind(Cell1=c("A", "B", "C"), Cell2=c("B","D","E), Strength= c(2, 0, -2)).
- same.dis.cutoff
(Default = 0) Cells with distance less than this cutoff will be considered as overlapping cells non-realistic in real ST data, and only one will be kept.
- even.distribution.coef
(Default =0). The higher the value, the more we require evenly distributed locations of cells, as opposed to randomly generated locations (Poisson process).
- grid.size.small
(Default =19). If some levels of even distributions of cells are imposed, this parameter is needed to cut the simulation window into grids of different sizes to smooth cell densities.
- grid.size.large
(Default =45). If some levels of even distributions of cells are imposed, this parameter is needed to cut the simulation window into grids of different sizes to smooth cell densities.
- seed
Random seed