
Placebo_Erythropoeitin_harmonised_data$celltypeCondition <- (paste(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data@meta.data$type, sep="_"))

Placebo_Erythropoeitin_harmonised_data$celltypes <- Idents(Placebo_Erythropoeitin_harmonised_data)

Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample <- (paste(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data@meta.data$orig.ident, sep="_"))

Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample
levels(Placebo_Erythropoeitin_harmonised_data)

dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data)
dim(dat)
head(dat)
dat <- as.data.frame(AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data))
dat <- as.matrix(AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data))
dim(dat)
head(dat)
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data)
dat.sct <- dat[["SCT"]]
head(dat.sct)
dat.rna <- dat[["RNA"]]
head(dat.rna)
head(Idents(Placebo_Erythropoeitin_harmonised_data))


dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data, group.by=Idents(Placebo_Erythropoeitin_harmonised_data))
head(Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample)
Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample <- gsub("_B12", "_B11", Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample)
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data, group.by=Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample)
Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample <- Idents(Placebo_Erythropoeitin_harmonised_data)
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data, group.by=Idents(Placebo_Erythropoeitin_harmonised_data))

Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$celltype_per_Sample
Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$celltypes
prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$orig.ident), margin = 2)*100


ct.smpl.prp <- prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$orig.ident), margin = 2)*100
ct.smpl.prp[10,]
ct.smpl.prp[11,]

Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$orig.ident
levels(Placebo_Erythropoeitin_harmonised_data)
Placebo_Erythropoeitin_harmonised_data_s1 <- subset(Placebo_Erythropoeitin_harmonised_data, idents = c("A1", "A2", "A3", "A4", "A6","B7", "B8", "B9", "B10", "B11"))


levels(Placebo_Erythropoeitin_harmonised_data_s1)
Idents(Placebo_Erythropoeitin_harmonised_data_s1) <- Placebo_Erythropoeitin_harmonised_data_s1$celltypes
levels(Placebo_Erythropoeitin_harmonised_data_s1)
Placebo_Erythropoeitin_harmonised_data_s1 <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("CA1_dorsal", "CA1_superficial", "CA1_Retrohippo", "New_born_CA1_deep_firing", "CA2", "CA3_dorsal","deep_layer_thin-CA3", "New_born_Ventral_CA3_serotonin", "New_born_CA3_superficial_Mbp", "New_born_migrating_superficial", "New_born_migrating_serotonin_firing", "New_born_migrating_superficial_Sox5", "New_born_migrating-deep_Sox5", "Ventral_CA1_migrating"))
)
Idents(Placebo_Erythropoeitin_harmonised_data_s1)
levels(Placebo_Erythropoeitin_harmonised_data_s1)
head(Placebo_Erythropoeitin_harmonised_data_s1$celltype_per_Sample)


dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data, group.by=Placebo_Erythropoeitin_harmonised_data_s1$celltype_per_Sample)
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_s1, group.by=Placebo_Erythropoeitin_harmonised_data_s1$celltype_per_Sample)
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_s1)
dat.rna <- dat[["RNA"]]
head(dat.rna)
dim(dat.rna)
head(Idents(Placebo_Erythropoeitin_harmonised_data_s1))
Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("CA1_dorsal"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
head(dat.rna)
dat.sct <- dat[["SCT"]]
head(dat.sct)
dim(dat.sct)
dim(dat.rna)



write.table(dat.rna, "CA1_dorsal_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "CA1_dorsal_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
history()
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("CA1_superficial"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "CA1_superficial_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "CA1_superficial_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("CA1_Retrohippo"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "CA1_Retrohippo_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "CA1_Retrohippo_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_CA1_deep_firing"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_CA1_deep_firing_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_CA1_deep_firing_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
  Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("CA2"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "CA2_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "CA2_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("CA3_dorsal"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "CA3_dorsal_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "CA3_dorsal_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("deep_layer_thin-CA3"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "deep_layer_thin-CA3_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "deep_layer_thin-CA3_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_Ventral_CA3_serotonin"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_Ventral_CA3_serotonin_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_Ventral_CA3_serotonin_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_CA3_superficial_Mbp"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_CA3_superficial_Mbp_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_CA3_superficial_Mbp_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_migrating_superficial"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_migrating_superficial_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_migrating_superficial_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_migrating_serotonin_firing"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_migrating_serotonin_firing_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_migrating_serotonin_firing_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_migrating_serotonin_firing_Sox5"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_migrating_serotonin_firing_Sox5_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_migrating_serotonin_firing_Sox5_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
levels(Placebo_Erythropoeitin_harmonised_data_s1)
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_migrating_superficial_Sox5"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_migrating_superficial_Sox5_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_migrating_superficial_Sox5_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("New_born_migrating-deep_Sox5"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "New_born_migrating-deep_Sox5_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "New_born_migrating-deep_Sox5_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
 
 Placebo_Erythropoeitin_harmonised_data_sub <- subset(Placebo_Erythropoeitin_harmonised_data_s1, idents = c("Ventral_CA1_migrating"))
 
dat <- AggregateExpression(object = Placebo_Erythropoeitin_harmonised_data_sub)
dat.rna <- dat[["RNA"]]
dat.sct <- dat[["SCT"]]
write.table(dat.rna, "Ventral_CA1_migrating_RNA_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
write.table(dat.sct, "Ventral_CA1_migrating_sct_Aggregate_expression_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)
levels(Idents(Placebo_Erythropoeitin_harmonised_data))
Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$celltypes
