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- library(dplyr)
- library(tidyr)
- time_points <- c("E14.5","E16.5","E18.5","P1","P4","P7")
- for(time_point in time_points){
- ## Load Seurat object
- seurat_object <- readRDS(paste("../Objects/",time_point,".Seurat_object.Rds",sep=""))
- ## Normalized expression data
- norm_exprs_sparse <- seurat_object@data
- norm_exprs_matrix <- as.matrix(seurat_object@data)
- norm_exprs_df <- as.data.frame(norm_exprs_matrix)
- ## Create a new data frame that contains tSNE embeddings and cluster identities
- tsne_mappings <- seurat_object@dr$tsne@cell.embeddings
- cell_identities <- data.frame(seurat_object@ident)
- rownames(cell_identities) <- names(seurat_object@ident)
- tsne_mappings <- merge(tsne_mappings,cell_identities,by=0,all=TRUE)
- rownames(tsne_mappings) <- tsne_mappings$Row.names
- tsne_mappings <- tsne_mappings %>%
- select(-Row.names)
- ## Metadata information
- metadata <- seurat_object@meta.data
- save(norm_exprs_df,tsne_mappings,metadata,
- file=paste("../Shiny_server_data/Clustering.",time_point,".RData",sep=""))
- }
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