Function to convert SpatialExperiment object to a data frame

Function to convert SpatialExperiment object to a data frame

Usage

.SPE2df(spe, imageCol = NULL, marks = NULL, colNames = FALSE)

Arguments

spe: SpatialExperiment; a object of class SpatialExperiment
imageCol: character; name of a column in colData that corresponds to the image
marks: character; name of column in colData with categorical marks
colNames: logical; extract colnames from SpatialExperiment

Value

data.frame with x, y coordinates, image, and categorical mark information

Examples

data(sostaSPE)
.SPE2df(sostaSPE, marks = "cellType", imageCol = "imageName") |> head()
#>            x         y cellType imageName
#> 1 113.964828  79.72171        A    image1
#> 2  18.828120  51.33354        A    image1
#> 3 119.718375  57.28533        A    image1
#> 4  38.557299 119.77972        A    image1
#> 5   7.772233  87.46652        A    image1
#> 6  18.213670  63.46682        A    image1