A wrapper for running the DOT algorithm for low-resolution spatial data with suggested parameters — run.DOT.lowresolution • DOT

A wrapper for running the DOT algorithm for low-resolution spatial data with suggested parameters

Usage

run.DOT.lowresolution(
  object,
  ratios_weight = 0,
  max_spot_size = 20,
  iterations = 100,
  verbose = FALSE
)

Arguments

object: A DOT object created using create.DOT().
ratios_weight: A value between 0 and 1 for matching ratio of cell types
max_spot_size: An upper bound on the size of spots. Default is 20, can be set to a higher value for lower resolution (eg, 200 for ST).
iterations: Integer. Maximum number of iterations of FW
verbose: Boolean. Whether progress should be displayed.

Value

A DOT object with the produced results contained in the weights slot

Examples

data(dot.sample)
dot.ref <- setup.ref(dot.sample$ref$counts[, 1:1000], dot.sample$ref$labels[1:1000], 2)
dot.srt <- setup.srt(dot.sample$srt$counts, dot.sample$srt$coordinates)
#> Computing spatial radius
dot <- create.DOT(dot.srt, dot.ref)
# No. iterations is reduced to 10 for this example (default is 100)
dot <- run.DOT.lowresolution(dot, iterations = 10)