Heart (ino80 mutant and wildtype)

# install.packages("Seurat")
# install.packages("svGUI")
# install.packages("svDialogs")
# install.packages("R.matlab")

remove(list = ls())

library(dplyr)
library(Seurat)
library(svDialogs)
library(R.matlab)

load(choose.files(default = paste0(getwd(), "/Data/*.Robj"), 
                  caption = "Select file to read", multi = FALSE))

New_Tiss <- UpdateSeuratObject(tiss)
New_Tiss <- RunUMAP(New_Tiss, dims = 1:15, verbose = FALSE)

TSNE <- New_Tiss@reductions[["tsne"]]@cell.embeddings
UMAP <- New_Tiss@reductions[["umap"]]@cell.embeddings


GCidx <- New_Tiss@assays[["RNA"]]@data@i
GCnum <- New_Tiss@assays[["RNA"]]@data@p
GCval <- New_Tiss@assays[["RNA"]]@data@x
GCdim <- New_Tiss@assays[["RNA"]]@data@Dim
GCsum <- New_Tiss@meta.data[["nReads"]]

GENE  <- New_Tiss@assays[["RNA"]]@data@Dimnames[[1]]
BCODE <- New_Tiss@assays[["RNA"]]@data@Dimnames[[2]]


META <- New_Tiss[[]]
Annotation <- META %>%select(mouse.id, cell_ontology_class)


SaveFolder <- choose.dir(default = paste0(getwd(), "/Output"))
writeMat(paste0(SaveFolder, '\\GC_Data.mat'), 
         GCidx = GCidx, GCval = GCval, GCnum = GCnum, GCdim = GCdim, GCsum = GCsum, TSNE = TSNE, UMAP = UMAP)

write.csv(GENE, paste0(SaveFolder, '\\Gene_Name.csv'))
write.csv(Annotation, paste0(SaveFolder, '\\Cell_Type.csv'))