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Enhance Seurat interoperability for Xenium dataset support #235

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Sep 23, 2024
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Enhance Seurat interoperability for Xenium dataset support #235

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53 changes: 32 additions & 21 deletions R/interoperability.R
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Original file line number Diff line number Diff line change
Expand Up @@ -767,15 +767,15 @@ giottoToAnnData <- function(gobject = NULL,
# Feat Metadata
for (su in spat_unit) {
for (ft in names(gobject@expression[[su]])) {
cmeta <- get_cell_metadata(
cmeta <- getCellMetadata(
gobject = gobject,
spat_unit = su,
feat_type = ft,
output = "data.table",
set_defaults = FALSE
)

fm <- get_feature_metadata(
fm <- getFeatureMetadata(
gobject = gobject,
spat_unit = su,
feat_type = ft,
Expand Down Expand Up @@ -1289,7 +1289,7 @@ giottoToSeuratV4 <- function(gobject,
}
# add cell metadata
meta_cells <- data.table::setDF(
get_cell_metadata(
getCellMetadata(
gobject = gobject,
spat_unit = spat_unit,
feat_type = assay_use,
Expand All @@ -1307,7 +1307,7 @@ giottoToSeuratV4 <- function(gobject,
)
# add feature metadata
meta_genes <- data.table::setDF(
get_feature_metadata(
getFeatureMetadata(
gobject = gobject,
spat_unit = spat_unit,
feat_type = assay_use,
Expand Down Expand Up @@ -1477,7 +1477,14 @@ giottoToSeuratV5 <- function(gobject,
gobject = gobject,
spat_unit = spat_unit
)

assay_names <- names(gobject@expression$cell)

# Identify assays with spaces and replace with underscores
new_assay_names <- gsub(" ", "_", assay_names)

# Apply the new names to the gobject expression slot
names(gobject@expression$cell) <- new_assay_names

# verify if optional package is installed
package_check(pkg_name = "Seurat", repository = "CRAN")
loadNamespace("Seurat")
Expand Down Expand Up @@ -1569,8 +1576,9 @@ giottoToSeuratV5 <- function(gobject,
}

# add cell metadata
names(gobject@cell_metadata$cell) <- gsub(" ", "_", names(gobject@cell_metadata$cell))
meta_cells <- data.table::setDF(
get_cell_metadata(
getCellMetadata(
gobject = gobject,
spat_unit = spat_unit,
feat_type = assay_use,
Expand All @@ -1579,21 +1587,22 @@ giottoToSeuratV5 <- function(gobject,
)
)
rownames(meta_cells) <- meta_cells$cell_ID
meta_cells <- meta_cells[, -which(colnames(meta_cells) == "cell_ID")]
meta_cells <- meta_cells[, -which(colnames(meta_cells) == "cell_ID"), drop = FALSE]
if (ncol(meta_cells) > 0) {
colnames(meta_cells) <- paste0(
assay_use, "_",
colnames(meta_cells)
)
}
sobj <- Seurat::AddMetaData(sobj,
metadata = meta_cells[Seurat::Cells(sobj), ],
col.name = names(meta_cells)
)

}

# add feature metadata
names(gobject@feat_metadata$cell) <- gsub(" ", "_", names(gobject@feat_metadata$cell))
meta_genes <- data.table::setDF(
get_feature_metadata(
getFeatureMetadata(
gobject = gobject,
spat_unit = spat_unit,
feat_type = assay_use,
Expand All @@ -1602,15 +1611,14 @@ giottoToSeuratV5 <- function(gobject,
)
)
rownames(meta_genes) <- meta_genes$feat_ID
for (i in seq_along(sobj@assays)) {
# Check if assay_slot has @meta.data or @meta.features
if ("meta.data" %in% slotNames(sobj@assays[[i]])) {
sobj@assays[[i]]@meta.data <- meta_genes
} else if ("meta.features" %in% slotNames(sobj@assays[[i]])) {
sobj@assays[[i]]@meta.features <- meta_genes
} else {
warning(paste("No suitable metadata slot found for assay", i))
}
if ("meta.data" %in% slotNames(sobj@assays[[assay_use]])) {
sobj@assays[[assay_use]]@meta.data <- meta_genes
message(paste("Meta data updated for assay:", assay_use))
} else if ("meta.features" %in% slotNames(sobj@assays[[assay_use]])) {
sobj@assays[[assay_use]]@meta.features <- meta_genes
message(paste("Meta features updated for assay:", assay_use))
} else {
warning(paste("No suitable metadata slot found for assay", assay_use))
}

# dim reduction
Expand Down Expand Up @@ -2331,15 +2339,18 @@ seuratToGiottoV5 <- function(sobject,
}
# Subcellular
name <- names(sobject@images)
# if (!is.null(subcellular_assay)){
if (length(sobject@assays[[subcellular_assay]]) == 1) {
if (!is.null(Seurat::Images(
object = sobject,
assay = spatial_assay
))) {
spat_coord <- Seurat::GetTissueCoordinates(sobject)
colnames(spat_coord) <- c("sdimx", "sdimy")
spat_coord$cell_ID <- rownames(spat_coord)
exp <- exp[, c(intersect(spat_coord$cell_ID, colnames(exp)))]
spat_loc <- spat_coord
}
}
# }
if (!length(sobject@images) == 0) {
for (i in names(sobject@images)) {
if ("molecules" %in% names(sobject@images[[i]]) == TRUE) {
Expand Down
69 changes: 69 additions & 0 deletions tests/testthat/test-interoperability.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
library(testthat)
library(Giotto)
library(Seurat)

giotto_obj <- GiottoData::loadGiottoMini("visium")
seurat_obj <- giottoToSeuratV5(giotto_obj)
spe_obj <- giottoToSpatialExperiment(giotto_obj)

Seurat_obj2 <- SeuratData::LoadData("stxBrain", type = "anterior1" )
giotto_obj2 <- seuratToGiottoV5(Seurat_obj2)

giotto_obj_roundtrip <- seuratToGiottoV5(seurat_obj, "rna")

test_that("giottotoseurat function handles basic conversion", {

# Basic checks
expect_s4_class(seurat_obj, "Seurat")
expect_true(!is.null([email protected]))
expect_equal(nrow([email protected]),
nrow(giotto_obj@cell_metadata$cell$rna@metaDT))

# Check if image slots are handled correctly
if ("images" %in% slotNames(giotto_obj)) {
expect_true(length(seurat_obj@images) > 0)
expect_equal(length(seurat_obj@images), length(giotto_obj@images))
expect_s4_class(giotto_obj_roundtrip@images$alignment, "giottoLargeImage")
expect_s4_class(seurat_obj@images$alignment, "VisiumV1")
}
})

test_that("Giotto to Seurat Conversion Works",{
expect_s4_class(seurat_obj, "Seurat")
})

test_that("Seurat to Giotto Conversion Works",{
expect_s4_class(giotto_obj, "giotto")
})

test_that("Assay names are converted correctly (no spaces)", {
# Check for spaces in Seurat assay names
assay_names <- names(seurat_obj@assays)
expect_false(any(grepl(" ", assay_names))) # No spaces should be present
})

test_that("Data is consistent after roundtrip conversion", {

identical(giotto_obj_roundtrip@expression, giotto_obj@expression)
# Check consistency of expression data
expect_equal(dim(giotto_obj@expression$cell$rna$raw),
dim(giotto_obj_roundtrip@expression$cell$rna$raw))

# Check consistency of cell metadata
expect_equal(nrow(giotto_obj@cell_metadata$cell$rna@metaDT),
nrow(giotto_obj_roundtrip@cell_metadata$cell$rna@metaDT))
})

test_that("Feature metadata is transferred correctly", {
# Check if feature metadata (e.g., gene names) is correctly transferred
expect_equal(rownames(seurat_obj@assays$rna),
rownames(giotto_obj@expression$cell$rna$raw))
})

test_that("Giotto to SpatialExperiment Conversion Works",{
expect_s4_class(spe_obj[[1]], "SpatialExperiment")
})

#TODO
#spe
#annData