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format_sce_to_ppp

Source: R/format_sce_to_ppp.R
format_sce_to_ppp.Rd

Formats an sce object into a ppp object which has the x,y coordinates, phenotypes as markers window specifies the range of x and y coordinates

Usage

format_sce_to_ppp(
  sce_object,
  window_pol = FALSE,
  feature_colname = "Phenotype"
)

Arguments

sce_object

SingleCellExperiment object in the form of the output of format_image_to_sce

window_pol

Optional Boolean Specifying if the window is polygon

feature_colname

String specifying the feature column of interest

Value

A ppp object is returned (defined in `spatstat` package)

Examples

ppp_object<-format_sce_to_ppp(SPIAT::defined_image, feature_colname = "Cell.Type")