# Testing functions of manipulating embeddings ####

test_that("add assay", {

  # get data

  data("xenium_data")

  # assay name and metadata

  assay <- vrAssayNames(xenium_data)

  sample_metadata <- SampleMetadata(xenium_data)

  # add cell assay

  new_assay <- formAssay(data = vrData(xenium_data),

                         coords = vrCoordinates(xenium_data), 

                         segments = vrSegments(xenium_data),

                         type = "cell",

                         image = vrImages(xenium_data),

                         main_image = vrMainImage(xenium_data[[assay]]),

                         name = assay)

  xenium_data2 <- addAssayVoltRon(xenium_data,

                                  assay = new_assay,

                                  assay_name = "Xenium",

                                  sample = sample_metadata[assay, "Sample"],

                                  layer = sample_metadata[assay, "Layer"])

  expect_equal(unique(Metadata(xenium_data2)$assay_id), c("Assay1", "Assay2"))

  # add cell assay with metadata

  metadata <- data.frame(points = vrSpatialPoints(xenium_data))

  xenium_data2 <- addAssayVoltRon(xenium_data,

                                   metadata = metadata,

                                   assay = new_assay,

                                   assay_name = "Xenium",

                                   sample = sample_metadata[assay, "Sample"],

                                   layer = sample_metadata[assay, "Layer"])

  expect_equal(unique(Metadata(xenium_data2)$assay_id), c("Assay1", "Assay2"))

  expect_true("points" %in% colnames(Metadata(xenium_data2)))

  # add ROI assay

  coords <- vrCoordinates(xenium_data)[1:2,,drop = FALSE]

  new_assay <- formAssay(coords = coords, 

                         segments = vrSegments(xenium_data)[1:2],

                         type = "ROI",

                         image = vrImages(xenium_data, assay = assay),

                         main_image = vrMainImage(xenium_data[[assay]]),

                         name = assay)

  metadata <- data.frame(check.rows = FALSE, row.names = rownames(coords), rep("art", nrow(coords)))

  colnames(metadata) <- "label"

  xenium_data2 <- addAssayVoltRon(xenium_data,

                                  assay = new_assay,

                                  metadata = metadata,

                                  assay_name = "random_ROI_assay",

                                  sample = sample_metadata[assay, "Sample"],

                                  layer = sample_metadata[assay, "Layer"])

  expect_true("label" %in% colnames(Metadata(xenium_data2, type = "ROI")))

  expect_true(nrow(Metadata(xenium_data2, type = "ROI")) == 2)

  # return

  expect_equal(1,1L)

})