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streamlined symbol conversion and throws an error for v5
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@csangara
csangara committed Mar 21, 2024
1 parent 21e261e commit 70d300e
Showing 1 changed file with 47 additions and 298 deletions.
345 changes: 47 additions & 298 deletions R/supporting_functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -212,333 +212,82 @@ convert_alias_to_symbols = function(aliases, organism, verbose = TRUE){
#' @export
#'
alias_to_symbol_seurat = function(seurat_obj, organism) {

requireNamespace("dplyr")
requireNamespace("Seurat")

RNA = seurat_obj@assays$RNA
newnames = convert_alias_to_symbols(rownames(RNA@counts), organism = organism, verbose = FALSE)

# sometimes: there are doubles:
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names

if (nrow(RNA) == length(newnames)) {

if(!is.null(RNA@counts)){
if(sum(dim(RNA@counts)) != 0) rownames(RNA@counts) = newnames
}
if(!is.null(RNA@data)){
if(sum(dim(RNA@data)) != 0){
newnames = convert_alias_to_symbols(rownames(RNA@data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(RNA@data) = newnames
}
}
if(!is.null(RNA@scale.data)){
if(sum(dim(RNA@scale.data)) != 0){
newnames = convert_alias_to_symbols(rownames(RNA@scale.data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(RNA@scale.data) = newnames
}
}

if (length(RNA@var.features) > 0){
newnames = convert_alias_to_symbols(RNA@var.features, organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
RNA@var.features = newnames
}

if (nrow(RNA@meta.features) > 0){
newnames = convert_alias_to_symbols(rownames(RNA@meta.features), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(RNA@meta.features) = newnames
}

} else {"Unequal gene sets: nrow(seurat_obj@assays$RNA) != nrow(newnames)"}

if(!is.null(RNA@counts)){
dim_before = dim(RNA@counts)
RNA@counts = RNA@counts %>% .[!is.na(rownames(.)), ]
dim_after = dim(RNA@counts)
if(sum(dim_before != dim_after) > 0){
print("dim counts assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
if(!is.null(RNA@data)){
dim_before = dim(RNA@data)
RNA@data = RNA@data %>% .[!is.na(rownames(.)), ]
dim_after = dim(RNA@data)
if(sum(dim_before != dim_after) > 0){
print("dim data assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
if(!is.null(RNA@scale.data)){
dim_before = dim(RNA@scale.data)
RNA@scale.data = RNA@scale.data %>% .[!is.na(rownames(.)), ]
dim_after = dim(RNA@scale.data)
if(sum(dim_before != dim_after) > 0){
print("dim scale.data assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}

if (length(RNA@var.features) > 0){
dim_before = length(RNA@var.features)
RNA@var.features = RNA@var.features %>% .[!is.na(.)]
dim_after = length(RNA@var.features)
if(dim_before != dim_after){
print("length of var.features changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
obj_version <- as.numeric(substr(seurat_obj@version, 1, 1))

if (nrow(RNA@meta.features) > 0){
dim_before = dim(RNA@meta.features)
RNA@meta.features = RNA@meta.features %>% .[!is.na(rownames(.)), ]
dim_after = dim(RNA@meta.features)
if(sum(dim_before != dim_after) > 0){
print("length of meta.features changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
# Stop if obj_version is seurat v5
if (obj_version >= 5){
stop("This function is not supported for Seurat v5 objects. Consider using `convert_alias_to_symbols` on your original expression matrix and creating a new Seurat object instead.
If this is not feasible, consider checking out Seurat.utils::RenameGenesSeurat.")
}

seurat_obj@assays$RNA = RNA
assays <- Assays(seurat_obj)

if(!is.null( seurat_obj@assays$SCT)){
SCT = seurat_obj@assays$SCT
newnames = convert_alias_to_symbols(rownames(SCT@counts), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
if (nrow(SCT) == length(newnames)) {

if(!is.null(SCT@counts)){
if(sum(dim(SCT@counts)) != 0){
rownames(SCT@counts) = newnames
}
}
if(!is.null(SCT@data)){
if(sum(dim(SCT@data)) != 0){
newnames = convert_alias_to_symbols(rownames(SCT@data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(SCT@data) = newnames
}
}
if(!is.null(SCT@scale.data)){
if(sum(dim(SCT@scale.data)) != 0){
newnames = convert_alias_to_symbols(rownames(SCT@scale.data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(SCT@scale.data) = newnames
}
}
convert_newnames <- function(feature_names, organism, verbose = FALSE) {
newnames <- convert_alias_to_symbols(feature_names, organism = organism, verbose = verbose)

if (length(SCT@var.features) > 0){
newnames = convert_alias_to_symbols(SCT@var.features, organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
SCT@var.features = newnames
}
# sometimes: there are doubles:
doubles <- newnames %>% table() %>% .[. > 1] %>% names()
genes_remove <-
(names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] <-
genes_remove # set the doubles back to their old names

if (nrow(SCT@meta.features) > 0){
newnames = convert_alias_to_symbols(rownames(SCT@meta.features), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(SCT@meta.features) = newnames
}
return(newnames)
}

} else {"Unequal gene sets: nrow(seurat_obj@assays$SCT) != nrow(newnames)"}
for (assay in assays) {
assay_obj <- GetAssay(seurat_obj, assay = assay)

if(!is.null(SCT@counts)){
dim_before = dim(SCT@counts)
SCT@counts = SCT@counts %>% .[!is.na(rownames(.)), ]
dim_after = dim(SCT@counts)
if(sum(dim_before != dim_after) > 0){
print("dim counts assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
if(!is.null(SCT@data)){
dim_before = dim(SCT@data)
SCT@data = SCT@data %>% .[!is.na(rownames(.)), ]
dim_after = dim(SCT@data)
if(sum(dim_before != dim_after) > 0){
print("dim data assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
if(!is.null(SCT@scale.data)){
dim_before = dim(SCT@scale.data)
SCT@scale.data = SCT@scale.data %>% .[!is.na(rownames(.)), ]
dim_after = dim(SCT@scale.data)
if(sum(dim_before != dim_after) > 0){
print("dim scale.data assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
slots <- c("counts", "data", "scale.data", "meta.features")
for (slot_name in slots) {
if (sum(dim(slot(assay_obj, slot_name))) != 0) {
newnames <- convert_newnames(rownames(slot(assay_obj, slot_name)),
organism = organism,
verbose = FALSE)

if (length(SCT@var.features) > 0){
dim_before = length(SCT@var.features)
SCT@var.features = SCT@var.features %>% .[!is.na(.)]
dim_after = length(SCT@var.features)
if(dim_before != dim_after){
print("length of var.features changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}

if (nrow(slot(assay_obj, slot_name)) == length(newnames)) {
rownames(slot(assay_obj, slot_name)) <- newnames

if (nrow(SCT@meta.features) > 0){
dim_before = dim(SCT@meta.features)
SCT@meta.features = SCT@meta.features %>% .[!is.na(rownames(.)), ]
dim_after = dim(SCT@meta.features)
if(sum(dim_before != dim_after) > 0){
print("length of meta.features changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
dim_before <- dim(slot(assay_obj, slot_name))
slot(assay_obj, slot_name) <-
slot(assay_obj, slot_name) %>% .[!is.na(rownames(.)),]
dim_after <- dim(slot(assay_obj, slot_name))

seurat_obj@assays$SCT = SCT
}
if (sum(dim_before != dim_after) > 0) {
print(paste0("dimensions of ", slot_name, " slot in ", assay," assay changed"))
print(paste0("before: ", dim_before))
print(paste0("after: ", dim_after))
}

if(!is.null( seurat_obj@assays$integrated)){
integrated = seurat_obj@assays$integrated
newnames = convert_alias_to_symbols(rownames(integrated@data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
if (nrow(integrated) == length(newnames)) {

if(!is.null(integrated@counts)){
if(sum(dim(integrated@counts)) != 0){
newnames = convert_alias_to_symbols(rownames(integrated@counts), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(integrated@counts) = newnames
}
}
if(!is.null(integrated@data)){
if(sum(dim(integrated@data)) != 0){
newnames = convert_alias_to_symbols(rownames(integrated@data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(integrated@data) = newnames
}
}
if(!is.null(integrated@scale.data)){
if(sum(dim(integrated@scale.data)) != 0){
newnames = convert_alias_to_symbols(rownames(integrated@scale.data), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(integrated@scale.data) = newnames
}
}

if (length(integrated@var.features) > 0){
newnames = convert_alias_to_symbols(integrated@var.features, organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
integrated@var.features = newnames
}
}

if (nrow(integrated@meta.features) > 0){
newnames = convert_alias_to_symbols(rownames(integrated@meta.features), organism = organism, verbose = FALSE)
doubles = newnames %>% table() %>% .[. > 1] %>% names()
genes_remove = (names(newnames[newnames %in% doubles]) != (newnames[newnames %in% doubles])) %>% .[. == TRUE] %>% names()
newnames[genes_remove] = genes_remove # set the doubles back to their old names
rownames(integrated@meta.features) = newnames
}

} else {"Unequal gene sets: nrow(seurat_obj@assays$integrated) != nrow(newnames)"}
if (length(assay_obj@var.features) > 0) {
newnames <- convert_newnames(assay_obj@var.features, organism = organism, verbose = FALSE)

if(!is.null(integrated@counts)){
dim_before = dim(integrated@counts)
integrated@counts = integrated@counts %>% .[!is.na(rownames(.)), ]
dim_after = dim(integrated@counts)
if(sum(dim_before != dim_after) > 0){
print("dim counts assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
if(!is.null(integrated@data)){
dim_before = dim(integrated@data)
integrated@data = integrated@data %>% .[!is.na(rownames(.)), ]
dim_after = dim(integrated@data)
if(sum(dim_before != dim_after) > 0){
print("dim data assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
if(!is.null(integrated@scale.data)){
dim_before = dim(integrated@scale.data)
integrated@scale.data = integrated@scale.data %>% .[!is.na(rownames(.)), ]
dim_after = dim(integrated@scale.data)
if(sum(dim_before != dim_after) > 0){
print("dim scale.data assay changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}
assay_obj@var.features <- newnames

if (length(integrated@var.features) > 0){
dim_before = length(integrated@var.features)
integrated@var.features = integrated@var.features %>% .[!is.na(.)]
dim_after = length(integrated@var.features)
if(dim_before != dim_after){
dim_before <- length(assay_obj@var.features)
assay_obj@var.features <-
assay_obj@var.features %>% .[!is.na(.)]
dim_after <- length(assay_obj@var.features)
if (dim_before != dim_after) {
print("length of var.features changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
print(paste0("before: ", dim_before))
print(paste0("after: ", dim_after))
}
}

if (nrow(integrated@meta.features) > 0){
dim_before = dim(integrated@meta.features)
integrated@meta.features = integrated@meta.features %>% .[!is.na(rownames(.)), ]
dim_after = dim(integrated@meta.features)
if(sum(dim_before != dim_after) > 0){
print("length of meta.features changed")
print(paste0("before: ",dim_before))
print(paste0("after: ",dim_before))
}
}

seurat_obj@assays$integrated = integrated
seurat_obj@assays[[assay]] <- assay_obj
}


return(seurat_obj)

}
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