Calculate the spatial diversity of base line metrics

Calculate the spatial diversity of base line metrics

calNegMarkerVsDist(
  spe,
  celltype,
  nn_celltype_pair,
  nn_neg_markers_list,
  exprs_threshold = 0,
  distance_breaks = c(seq(0, 50, 10), 100),
  exprs_values = "logcounts"
)

Arguments

spe

A Spatial Experiment object

celltype

A string or a vector indicating the cell type information. If it is a string, it will retrive the information from colData.

nn_celltype_pair

A pair of cell type.

nn_neg_markers_list

A list of negative marker corresponding to each cell type in `nn_celltype_pair`.

exprs_threshold

A numeric indicating the threshold to be considered as expressed.

distance_breaks

A numeric vector of two or more unique cut points for distance between the pair of cell type.

exprs_values

A string indicating which assay of `spe` contains the expression values.

Value

A SpatialExperiment object