Create a CoPro object, automatically choosing Single vs Multi and splitting large slices.

Behavior:

1. one slice and ncell < p -> newCoProSingle()

2. one slice and ncell > p -> newCoProMulti() with artificial blocks

3. multi slices, all < p -> newCoProMulti() with original slideID

4. multi slices, some > p -> newCoProMulti() with refined slideID (origin + block)

Usage

CreateCoPro(
  normalizedData,
  locationData,
  metaData,
  cellTypes,
  slideID = NULL,
  maxCell = 50000L,
  plot = FALSE,
  seed = 1L
)

Arguments

normalizedData

matrix (cells x genes)

locationData

data.frame (cells x coords; needs x,y, optionally z)

metaData

data.frame (cells x annotations)

cellTypes

vector length nrow(normalizedData)

slideID

optional vector length nrow(normalizedData); if NULL, treated as one slice

maxCell

integer max cells per (sub)slice (default 50000)

plot

logical; if TRUE, plot the auto-slicing result (default FALSE)

seed

integer seed for reproducible splitting (default 1)