Create .Rdata file from Seurat object for clustering module of shiny server (for .Rdata)

extract_shiny_data.R

library(dplyr)
library(tidyr)

time_point <- readline(prompt="Enter time point: ")

## 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=""))