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Updating for Seurat V5 compatibility #47

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c93ad09
Fixing data retrieval of sobj
MVesuviusC Aug 17, 2026
6d50dc0
updating how gene names are pulled
MVesuviusC Aug 17, 2026
a91a35b
Updating how traint() updates layer data
MVesuviusC Aug 17, 2026
41d9be2
updating how counts layer is zero'd out in traint sobj
MVesuviusC Aug 17, 2026
7046d04
updating code in celltrek() to work with Seurat V5
MVesuviusC Aug 20, 2026
9c67024
Fixing seurat functions in celltrek_dist and celltrek_from_dist
MVesuviusC Aug 20, 2026
5506121
Merge pull request #1 from MVesuviusC/try_fix
MVesuviusC Aug 20, 2026
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53 changes: 26 additions & 27 deletions R/celltrek.R
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Original file line number Diff line number Diff line change
Expand Up @@ -43,28 +43,27 @@ traint <- function (st_data, sc_data, st_assay='Spatial', sc_assay='scint', norm
sc_st_features <- union(sc_st_features, gene_kept)
}

sc_st_features <- sc_st_features[(sc_st_features %in% rownames(st_data[[st_assay]]@data)) &
(sc_st_features %in% rownames(sc_data[[sc_assay]]@data))]
sc_st_features <- sc_st_features[(sc_st_features %in% rownames(GetAssayData(st_data, assay = st_assay, layer = "data"))) &
(sc_st_features %in% rownames(Seurat::GetAssayData(sc_data, assay = sc_assay, layer = "data")))]
cat('Using', length(sc_st_features), 'features for integration... \n')
###

sc_st_anchors <- Seurat::FindTransferAnchors(reference = sc_data, query = st_data,
reference.assay = sc_assay, query.assay = st_assay,
normalization.method = norm, features = sc_st_features, reduction = 'cca', ...)

cat('Data transfering... \n')
st_data_trans <- Seurat::TransferData(anchorset = sc_st_anchors,
refdata = GetAssayData(sc_data, assay = sc_assay, slot='data')[sc_st_features, ], weight.reduction = 'cca')
refdata = GetAssayData(sc_data, assay = sc_assay, layer='data')[sc_st_features, ], weight.reduction = 'cca')
st_data@assays$transfer <- st_data_trans

cat('Creating new Seurat object... \n')
sc_st_meta <- dplyr::bind_rows(st_data@meta.data, sc_data@meta.data)
counts_temp <- cbind(data.frame(st_data[['transfer']]@data), data.frame(sc_data[[sc_assay]]@data[sc_st_features, ] %>% data.frame))
counts_temp <- cbind(data.frame(st_data[['transfer']]@data), data.frame(Seurat::GetAssayData(sc_data, assay = sc_assay, layer = "data")[sc_st_features, ] %>% data.frame))
rownames(sc_st_meta) <- make.names(sc_st_meta$id)
colnames(counts_temp) <- make.names(sc_st_meta$id)
sc_st_int <- CreateSeuratObject(counts = counts_temp, assay = 'traint', meta.data = sc_st_meta)
sc_st_int[['traint']]@data <- sc_st_int[['traint']]@counts
sc_st_int[['traint']]@counts <- matrix(NA, nrow = 0, ncol = 0)
sc_st_int <- SetAssayData(sc_st_int, assay = "traint", layer = "data", new.data = GetAssayData(sc_st_int, assay = "traint", layer = "counts"))
sc_st_int <- SetAssayData(sc_st_int, assay = "traint", layer = "counts", new.data = matrix(NA, nrow = nrow(sc_st_int), ncol = ncol(sc_st_int)))

cat('Scaling -> PCA -> UMAP... \n')
sc_st_int <- ScaleData(sc_st_int, features = sc_st_features) %>%
Expand Down Expand Up @@ -144,7 +143,7 @@ celltrek_dist <- function (st_sc_int, int_assay='traint', reduction='pca', intp
sc_idx <- st_sc_int$id[st_sc_int$type=='sc']
meta_df <- data.frame(st_sc_int@meta.data)

st_sc_int_pca <- st_sc_int@reductions[[reduction]]@cell.embeddings[, 1:nPCs] %>% data.frame %>%
st_sc_int_pca <- Embeddings(st_sc_int, reduction = reduction)[, 1:nPCs] %>% data.frame %>%
mutate(id=st_sc_int$id, type=st_sc_int$type, class=st_sc_int$cell_names,
coord_x=st_sc_int$coord_x, coord_y=st_sc_int$coord_y)
st_pca <- st_sc_int_pca %>% dplyr::filter(type=='st') %>% dplyr::select(-c(id:class))
Expand Down Expand Up @@ -284,7 +283,7 @@ celltrek_from_dist <- function (dist_mat, coord_df, dist_cut, top_spot=10, spot_
sc_coord_list <- celltrek_chart(dist_mat=dist_mat, coord_df=coord_df, dist_cut=dist_cut, top_spot=top_spot, spot_n=spot_n, repel_r=repel_r, repel_iter=repel_iter)
sc_coord_raw <- sc_coord_list[[1]]
sc_coord <- sc_coord_list[[2]]
sc_out <- CreateSeuratObject(counts=sc_data[[sc_assay]]@data[, sc_coord$id_raw] %>% set_colnames(sc_coord$id_new),
sc_out <- CreateSeuratObject(counts=GetAssayData(sc_data, assay=sc_assay, layer="data")[, sc_coord$id_raw] %>% set_colnames(sc_coord$id_new),
project='celltrek', assay=sc_assay,
meta.data=sc_data@meta.data[sc_coord$id_raw, ] %>%
dplyr::rename(id_raw=id) %>%
Expand Down Expand Up @@ -361,16 +360,16 @@ celltrek <- function (st_sc_int, int_assay='traint', sc_data=NULL, sc_assay='RNA
if (!is.null(sc_data)) {
cat('sc data...')
sc_data$id <- Seurat::Cells(sc_data)
sc_out <- CreateSeuratObject(counts=sc_data[[sc_assay]]@data[, sc_coord$id_raw] %>% set_colnames(sc_coord$id_new),
sc_out <- CreateSeuratObject(counts=GetAssayData(sc_data, assay=sc_assay, layer="data")[, sc_coord$id_raw] %>% set_colnames(sc_coord$id_new),
project='celltrek', assay=sc_assay,
meta.data=sc_data@meta.data[sc_coord$id_raw, ] %>%
dplyr::rename(id_raw=id) %>%
mutate(id_new=sc_coord$id_new) %>%
set_rownames(sc_coord$id_new))
sc_out@meta.data <- dplyr::left_join(sc_out@meta.data, sc_coord) %>% data.frame %>% set_rownames(sc_out$id_new)

sc_out[[sc_assay]]@data <- sc_out[[sc_assay]]@counts
sc_out[[sc_assay]]@counts <- matrix(nrow = 0, ncol = 0)
sc_out <- SetAssayData(sc_out, layer="data", new.data=GetAssayData(sc_out, assay=sc_assay, layer="counts"))
sc_out <- SetAssayData(sc_out, layer="counts", new.data=matrix(nrow=nrow(sc_out), ncol=ncol(sc_out)))
sc_coord_raw_df <- CreateDimReducObject(embeddings=sc_coord_raw %>%
dplyr::mutate(coord1=coord_y, coord2=max(coord_x)+min(coord_x)-coord_x) %>%
dplyr::select(c(coord1, coord2)) %>% set_rownames(sc_coord_raw$id_new) %>% as.matrix,
Expand All @@ -381,24 +380,24 @@ celltrek <- function (st_sc_int, int_assay='traint', sc_data=NULL, sc_assay='RNA
assay=sc_assay, key='celltrek')
sc_out@reductions$celltrek <- sc_coord_dr
sc_out@reductions$celltrek_raw <- sc_coord_raw_df
if ('pca' %in% names(sc_data@reductions)) {
sc_pca_dr <- CreateDimReducObject(embeddings=sc_data@reductions$pca@cell.embeddings[sc_coord$id_raw, ] %>%
if ('pca' %in% Reductions(sc_data)) {
sc_pca_dr <- CreateDimReducObject(embeddings=Embeddings(sc_data, reduction = "pca")[sc_coord$id_raw, ] %>%
set_rownames(sc_coord$id_new) %>% as.matrix, assay=sc_assay, key='pca')
sc_out@reductions$pca <- sc_pca_dr
}
if ('umap' %in% names(sc_data@reductions)) {
sc_umap_dr <- CreateDimReducObject(embeddings=sc_data@reductions$umap@cell.embeddings[sc_coord$id_raw, ] %>%
if ('umap' %in% Reductions(sc_data)) {
sc_umap_dr <- CreateDimReducObject(embeddings=Embeddings(sc_data, reduction = "umap")[sc_coord$id_raw, ] %>%
set_rownames(sc_coord$id_new) %>% as.matrix, assay=sc_assay, key='umap')
sc_out@reductions$umap <- sc_umap_dr
}
if ('tsne' %in% names(sc_data@reductions)) {
sc_tsne_dr <- CreateDimReducObject(embeddings=sc_data@reductions$tsne@cell.embeddings[sc_coord$id_raw, ] %>%
if ('tsne' %in% Reductions(sc_data)) {
sc_tsne_dr <- CreateDimReducObject(embeddings=Embeddings(sc_data, reduction = "tsne")[sc_coord$id_raw, ] %>%
set_rownames(sc_coord$id_new) %>% as.matrix, assay=sc_assay, key='tsne')
sc_out@reductions$tsne <- sc_tsne_dr
}
} else {
cat('no sc data...')
sc_out <- CreateSeuratObject(counts=st_sc_int[[int_assay]]@data[, sc_coord$id_raw] %>%
sc_out <- CreateSeuratObject(counts=GetAssayData(st_sc_int, assay = int_assay, layer = "data")[, sc_coord$id_raw] %>%
set_colnames(sc_coord$id_new),
project='celltrek', assay=int_assay,
meta.data=st_sc_int@meta.data[sc_coord$id_raw, ] %>%
Expand All @@ -408,8 +407,8 @@ celltrek <- function (st_sc_int, int_assay='traint', sc_data=NULL, sc_assay='RNA
sc_out$coord_x <- sc_coord$coord_x[match(sc_coord$id_new, sc_out$id_new)]
sc_out$coord_y <- sc_coord$coord_y[match(sc_coord$id_new, sc_out$id_new)]

sc_out[[int_assay]]@counts <- matrix(nrow = 0, ncol = 0)
sc_out[[int_assay]]@scale.data <- st_sc_int[[int_assay]]@scale.data[, sc_coord$id_raw] %>% set_colnames(sc_coord$id_new)
sc_out <- SetAssayData(sc_out, layer="counts", new.data=matrix(nrow=nrow(sc_out), ncol=ncol(sc_out)))
sc_out <- SetAssayData(sc_out, layer="scale.data", new.data=GetAssayData(sc_out, assay=sc_assay, layer="scale.data")[, sc_coord$id_raw] %>% set_colnames(sc_coord$id_new))
sc_coord_raw_df <- CreateDimReducObject(embeddings=sc_coord_raw %>%
dplyr::mutate(coord1=coord_y, coord2=max(coord_x)+min(coord_x)-coord_x) %>%
dplyr::select(c(coord1, coord2)) %>% set_rownames(sc_coord_raw$id_new) %>% as.matrix,
Expand All @@ -422,18 +421,18 @@ celltrek <- function (st_sc_int, int_assay='traint', sc_data=NULL, sc_assay='RNA
assay=int_assay, key='celltrek')
sc_out@reductions$celltrek <- sc_coord_dr
sc_out@reductions$celltrek_raw <- sc_coord_raw_df
if ('pca' %in% names(st_sc_int@reductions)) {
sc_pca_dr <- CreateDimReducObject(embeddings=st_sc_int@reductions$pca@cell.embeddings[sc_coord$id_raw, ] %>%
if ('pca' %in% Reductions(sc_data)) {
sc_pca_dr <- CreateDimReducObject(embeddings=Embeddings(sc_data, reduction = "pca")[sc_coord$id_raw, ] %>%
set_rownames(sc_coord$id_new) %>% as.matrix, assay=int_assay, key='pca')
sc_out@reductions$pca <- sc_pca_dr
}
if ('umap' %in% names(st_sc_int@reductions)) {
sc_umap_dr <- CreateDimReducObject(embeddings=st_sc_int@reductions$umap@cell.embeddings[sc_coord$id_raw, ] %>%
if ('umap' %in% Reductions(sc_data)) {
sc_umap_dr <- CreateDimReducObject(embeddings=Embeddings(sc_data, reduction = "umap")[sc_coord$id_raw, ] %>%
set_rownames(sc_coord$id_new) %>% as.matrix, assay=int_assay, key='umap')
sc_out@reductions$umap <- sc_umap_dr
}
if ('tsne' %in% names(st_sc_int@reductions)) {
sc_tsne_dr <- CreateDimReducObject(embeddings=st_sc_int@reductions$tsne@cell.embeddings[sc_coord$id_raw, ] %>%
if ('tsne' %in% Reductions(sc_data)) {
sc_tsne_dr <- CreateDimReducObject(embeddings=Embeddings(sc_data, reduction = "tsne")[sc_coord$id_raw, ] %>%
set_rownames(sc_coord$id_new) %>% as.matrix, assay=int_assay, key='tsne')
sc_out@reductions$tsne <- sc_tsne_dr
}
Expand Down