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Added support for spatial locations from dim reduction #790

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Nov 8, 2023
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Added support for spatial locations from dim reduction #790

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142 changes: 107 additions & 35 deletions R/interoperability.R
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Original file line number Diff line number Diff line change
Expand Up @@ -984,6 +984,10 @@ giottoToSeuratV4 <- function(gobject,
spat_unit = NULL,
obj_use = NULL,
...){

#To use Seurat v4 assays
options(Seurat.object.assay.version = 'v4')

# data.table vars
feat_type = name = dim_type = nn_type = NULL
if(!is.null(obj_use)) {
Expand Down Expand Up @@ -1092,7 +1096,13 @@ giottoToSeuratV4 <- function(gobject,
)
)
rownames(meta_genes) <- meta_genes$feat_ID
sobj[[assay_use]]@meta.features <- cbind(sobj[[assay_use]]@meta.features,meta_genes)
if ("meta.data" %in% slotNames(sobj[[assay_use]])) {
sobj[[assay_use]]@meta.data <- cbind(sobj[[assay_use]]@meta.data, meta_genes)
}
else if ("meta.features" %in% slotNames(sobj[[assay_use]])){
sobj[[assay_use]]@meta.features <- cbind(sobj[[assay_use]]@meta.features,meta_genes)
}

# dim reduction
# note: Seurat requires assay name specification for each dim reduc
avail_dr = list_dim_reductions(gobject = gobject, spat_unit = spat_unit, feat_type = assay_use,)
Expand Down Expand Up @@ -1216,6 +1226,10 @@ giottoToSeuratV5 <- function(gobject,
obj_use = NULL,
...){

#To use new Seurat v5 assays
options(Seurat.object.assay.version = 'v5')


# data.table vars
feat_type = name = dim_type = nn_type = NULL

Expand Down Expand Up @@ -1463,6 +1477,7 @@ seuratToGiottoV4 = function(sobject,
dim_reduction = c('pca','umap'),
subcellular_assay = 'Vizgen'){
package_check('Seurat')

if(is.null(Seurat::GetAssayData(object = sobject, slot = "counts", assay = spatial_assay))) {
wrap_msg('No raw expression values are provided in spatial_assay')
return(sobject)
Expand All @@ -1471,8 +1486,10 @@ seuratToGiottoV4 = function(sobject,
if(!is.null(sobject@assays$SCT)){
normexp = Seurat::GetAssayData(object = sobject, slot = "counts", assay = 'SCT')
}
if ("data" %in% slotNames(slot(sobject, 'assays')[[spatial_assay]])){
if(!is.null(slot(sobject, 'assays')[[spatial_assay]]@data)){
normexp = Seurat::GetAssayData(object = sobject, slot = "data", assay = spatial_assay)
}
}
# Cell Metadata
cell_metadata = [email protected]
Expand Down Expand Up @@ -1504,9 +1521,9 @@ seuratToGiottoV4 = function(sobject,
# names(dimReduc_list) <- dim_reduction
}
# Spatial Locations
if(length(sobject@assays[[spatial_assay]]) == 0) {
spat_loc = NULL
} else {
# if(length(sobject@assays[[spatial_assay]]) == 0) {
# spat_loc = NULL
# } else {

# !requires image objects!
if (!is.null(Seurat::Images(object = sobject, assay = spatial_assay))) {
Expand All @@ -1516,35 +1533,56 @@ seuratToGiottoV4 = function(sobject,
spat_loc = spat_coord
} else {
message("Images for RNA assay not found in the data. Skipping image processing.")
spat_loc = NULL
# spat_loc = NULL
}

# }
if (length(sobject@assays[[spatial_assay]]) == 0 || is.null(Seurat::Images(object = sobject, assay = spatial_assay))) {
spat_loc <- data.frame(
sdimx = rep(0, length(colnames(sobject))),
sdimy = rep(0, length(colnames(sobject)))
)
}


# Subcellular
name = names(sobject@images)
if(length(sobject@assays[[subcellular_assay]]) == 1) {
spat_coord = Seurat::GetTissueCoordinates(sobject)
colnames(spat_coord) = c("sdimx", "sdimy", "cell_ID")
exp = exp[ , c(intersect(spat_coord$cell_ID, colnames(exp)))]
spat_loc = spat_coord
}
if (!length(sobject@images) == 0) {
if ("molecules" %in% methods::slotNames(sobject@images[[name]]) == TRUE) {
if(!length(sobject@images[[name]][["molecules"]]) == 0) {
assay = names(sobject@assays)
featnames = rownames(sobject@assays[[assay]]@meta.features)
mol_spatlocs = data.table::data.table()
for (x in featnames) {
df = (Seurat::FetchData(sobject[[name]][["molecules"]], vars = x))
mol_spatlocs = rbind(mol_spatlocs, df)
}
gpoints = createGiottoPoints(mol_spatlocs, feat_type = "rna")
}
}
}
# if(length(sobject@assays[[subcellular_assay]]) == 1) {
# spat_coord = Seurat::GetTissueCoordinates(sobject)
# colnames(spat_coord) = c("sdimx", "sdimy", "cell_ID")
# exp = exp[ , c(intersect(spat_coord$cell_ID, colnames(exp)))]
# spat_loc = spat_coord
# }

# if (!length(sobject@images) == 0) {
# if ("molecules" %in% methods::slotNames(sobject@images[[name]]) == TRUE) {
# if(!length(sobject@images[[name]][["molecules"]]) == 0) {
# assay = names(sobject@assays)
# featnames = rownames(sobject@assays[[assay]]@meta.features)
# mol_spatlocs = data.table::data.table()
# for (x in featnames) {
# df = (Seurat::FetchData(sobject[[name]][["molecules"]], vars = x))
# mol_spatlocs = rbind(mol_spatlocs, df)
# }
# gpoints = createGiottoPoints(mol_spatlocs, feat_type = "rna")
# }
# }
# }
}

if (length(sobject@assays[[subcellular_assay]]) == 0) {
cat("No subcellular information found.\n")
}
else{
cat("Please use function \"seuratToGiottoV5\" for handling subcellular information.\n")
}
if (length(sobject@images) == 0) {
cat("No images found\n")
}
else{
cat("Please use function \"seuratToGiottoV5\" for handling image information.\n")
}

gobject = createGiottoObject(exp,
spatial_locs = spat_loc,
dimension_reduction = dimReduc_list)
Expand Down Expand Up @@ -1578,9 +1616,9 @@ seuratToGiottoV4 = function(sobject,
seuratToGiottoV5 = function(sobject,
spatial_assay = 'Spatial',
dim_reduction = c('pca','umap'),
subcellular_assay = 'Vizgen'){
subcellular_assay = 'Vizgen',
spatial_loc = 'spatial'){
package_check('Seurat')

if(is.null(Seurat::GetAssayData(object = sobject, slot = "counts", assay = spatial_assay))) {
wrap_msg('No raw expression values are provided in spatial_assay')
return(sobject)
Expand Down Expand Up @@ -1609,20 +1647,24 @@ seuratToGiottoV5 = function(sobject,
feat_metadata = sobject[[]]

# Dimension Reduction
if(sum(sapply(dim_reduction,function(x) length(sobject@reductions[[x]]))) == 0) {
if (sum(sapply(dim_reduction, function(x) length(sobject@reductions[[x]]))) == 0) {
dimReduc_list = NULL
} else {
dimReduc_list = lapply(dim_reduction,function(x){
dim_coord = as.matrix(Seurat::Embeddings(object = sobject,reduction = x))
dimReduc_list = lapply(dim_reduction, function(x) {
dim_coord = as.matrix(Seurat::Embeddings(object = sobject, reduction = x))
dim_load = as.matrix(Seurat::Loadings(object = sobject, reduction = x))
dim_eig = Seurat::Stdev(sobject, reduction = x)
if (length(dim_eig) > 0){
dim_eig = sapply(dim_eig, function(x) x ^ 2)

if (length(dim_eig) > 0) {
dim_eig = sapply(dim_eig, function(y) y ^ 2)
}
colnames(dim_coord) = paste0('Dim.',1:ncol(dim_coord))
if (length(dim_load) > 0){
colnames(dim_load) = paste0('Dim.',1:ncol(dim_load))

colnames(dim_coord) = paste0('Dim.', 1:ncol(dim_coord))

if (length(dim_load) > 0) {
colnames(dim_load) = paste0('Dim.', 1:ncol(dim_load))
}

dimReduc = create_dim_obj(name = x,
reduction = 'cells',
reduction_method = x,
Expand All @@ -1635,6 +1677,8 @@ seuratToGiottoV5 = function(sobject,
return(dimReduc)
})
# names(dimReduc_list) <- dim_reduction
# 'dimReduc_list' now contains the list of 'dimReduc' objects for each element in 'dim_reduction'

}

# Spatial Locations
Expand Down Expand Up @@ -1732,7 +1776,29 @@ seuratToGiottoV5 = function(sobject,
}
}
}
if(length(spatial_loc) != 0){
if(spatial_loc %in% names(sobject@reductions)){
cell_ID <- rownames(sobject@reductions[[spatial_loc]])
spat_reduct <- cbind(sobject@reductions[[spatial_loc]]@cell.embeddings, cell_ID)
colnames(spat_reduct) <- c("sdimx", "sdimy", "cell_ID")
spat_loc <- spat_reduct
spat_loc <- as.data.frame(spat_loc)
length_assay <-length(colnames(sobject))
spat_datatable <- data.table(cell_ID = character(length_assay),
sdimx = rep(NA_real_, length_assay),
sdimy = rep(NA_real_, length_assay))

spat_datatable$cell_ID <- colnames(sobject)
match_cell_ID <- match(spat_loc$cell_ID, spat_datatable$cell_ID)
matching_indices <- match_cell_ID
matching_indices <- matching_indices[!is.na(matching_indices)]
spat_datatable[matching_indices, c("sdimx", "sdimy") := list(as.numeric(spat_loc$sdimx),as.numeric(spat_loc$sdimy))]
spat_loc <- spat_datatable
}
else{
message("spatial_loc: '", spatial_loc, "' spatial location were not found in the object")
}
}
#Find SueratImages, extract them, and pass to create seuratobj

for (i in names(sobject@images)){
Expand All @@ -1758,6 +1824,12 @@ seuratToGiottoV5 = function(sobject,
}
}

if (is.null(spat_loc)) {
spat_loc <- data.frame(
sdimx = rep(0, length(colnames(sobject))),
sdimy = rep(0, length(colnames(sobject)))
)
}

gobject = createGiottoObject(exp,
spatial_locs = spat_loc,
Expand Down
3 changes: 2 additions & 1 deletion man/seuratToGiottoV5.Rd
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