tests/testthat/apps/images_app_ondisk/app.R

In BodenmillerGroup/SingleCellMapper: Visualization of highly multiplexed imaging data in R

library(cytomapper)
data("pancreasSCE")
data("pancreasMasks")
data("pancreasImages")

cur_path <- tempdir()
on.exit(unlink(cur_path))

cur_Images <- CytoImageList(pancreasImages, on_disk = TRUE, h5FilesPath = cur_path)
cur_Masks <- CytoImageList(pancreasMasks, on_disk = TRUE, h5FilesPath = cur_path)

cytomapperShiny(object = pancreasSCE, mask = cur_Masks, 
                image = cur_Images,
                cell_id = "CellNb", img_id = "ImageNb")