I have a Seurat object made from integrating 4 different objects, the results is a Seurat object with 70 clusters (0 to 69) I wanted to subset each single cluster and recluster it to achieve higher resolution. here is the code I wrote, however, I keep getting an error. would you know what this could be ? thank you
here there is the code
clusters_to_subset <- 0:69
for (cluster_to_subset in clusters_to_subset) {
#Step 1: Identify cells from the specific cluster
cells_to_subset <- WhichCells(full_seurat_object, ident = clusters_to_subset)
#Step 2: Create a new Seurat object with subsetted cells
sub_seurat_object <- subset(full_seurat_object, cells = cells_to_subset)
#Step 3: Recluster the subsetted Seurat object with increased resolution
sub_seurat_object <- FindNeighbors(sub_seurat_object, dims = 1:30) # You can adjust 'dims' based on your data
sub_seurat_object <- FindClusters(sub_seurat_object, resolution = 1.5) # Adjust 'resolution' as needed
#Plot or save the new clustering results if desired
plot(sub_seurat_object, label = TRUE)
#Save the ggplot2 in .pdf format
ggsave(paste0("/Users/avolaa/Documents/Single_Cell_Paper/Species_Integration_Seurat/All_species_20230102/Seurat_Subset_Plots_20230102/Subset_clusters_", cluster_to_subset, ".pdf"))
#Save the ggplot2 in .png format
ggsave(paste0("/Users/avolaa/Documents/Single_Cell_Paper/Species_Integration_Seurat/All_species_20230102/Seurat_Subset_Plots_20230102/Subset_clusters_", cluster_to_subset, ".png"))
#Save the sub Seurat object or do any further processing as needed
saveRDS(sub_seurat_object, file = paste0("subset_cluster_", cluster_to_subset, ".rds"))
}
this is the error
Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double'
thank you!