Utility function to convert a SpatialExperiment object to a Giotto object

Utility function to convert a SpatialExperiment object to a Giotto object

Usage

spatialExperimentToGiotto(
  spe,
  python_path,
  nn_network = NULL,
  sp_network = NULL,
  verbose = TRUE
)

Arguments

spe

Input SpatialExperiment object to convert to a Giotto object.

python_path

Specify the path to python.

nn_network

Specify the name of the nearest neighbour network(s) in the input SpatialExperiment object. Default NULL will use all existing networks.

sp_network

Specify the name of the spatial network(s) in the input SpatialExperiment object. Default NULL will use all existing networks. This can be a vector of multiple network names.

verbose

A boolean value specifying if progress messages should be displayed or not. Default TRUE.

Value

Giotto object

Examples

if (FALSE) {
library(SpatialExperiment)
example(read10xVisium, echo = FALSE)
spatialExperimentToGiotto(spe)
}