prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$orig.ident), margin = 2)*100
proportion <- prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$orig.ident), margin = 2)*100
write.table(proportion, "Proportion_celltypes_Pyramidal_across_samples.tsv", row.names=T, col.names=NA, sep="\t", quote=F)



levels(Placebo_Erythropoeitin_harmonised_data)
head(Placebo_Erythropoeitin_harmonised_data$celltypeCondition)
head(Placebo_Erythropoeitin_harmonised_data$celltypes)
levels(Placebo_Erythropoeitin_harmonised_data$celltypes)
Placebo_Erythropoeitin_harmonised_data$broad_celltypes <- Idents(Placebo_Erythropoeitin_harmonised_data)
Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$celltypes

 
 
 names(new.cluster.ids) <- levels(Placebo_Erythropoeitin_harmonised_data)
 Placebo_Erythropoeitin_harmonised_data <- RenameIdents(Placebo_Erythropoeitin_harmonised_data, new.cluster.ids)
 levels(Placebo_Erythropoeitin_harmonised_data)
proportion <- prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$orig.ident), margin = 2)*100
write.table(proportion, "Proportion_celltypes_Pyramidal_across_samples_V2.tsv", row.names=T, col.names=NA, sep="\t", quote=F)

Idents(Placebo_Erythropoeitin_harmonised_data) <- Placebo_Erythropoeitin_harmonised_data$celltypes
new.cluster.ids <- c("CA1", "CA1_superficial", "CA1_retroHippo", "CA1_Newly_formed",  "CA2", 
                     "CA3", "CA3", "CA3", "CA3_Newly_formed", "Newly_formed_migrating",
                     "Newly_formed_migrating", "Newly_formed_migrating", "Newly_formed_migrating", "Newly_formed_migrating", "Newly_formed_Foxp2",
                     "Others", "Granule", "Others", "Others", "Others", "Others")
 
 
 names(new.cluster.ids) <- levels(Placebo_Erythropoeitin_harmonised_data)
 Placebo_Erythropoeitin_harmonised_data <- RenameIdents(Placebo_Erythropoeitin_harmonised_data, new.cluster.ids)
 levels(Placebo_Erythropoeitin_harmonised_data)


my_col <- c("maroon", "plum4", "coral", 
            "orange", "royalblue3", "darkorchid", 
            "gold", "darkturquoise", "black",
               "rosybrown1","seagreen")
               
               
png("Harmonised_New_lineages_Only_Pyra_UMAP_broad_celltypes.png",  width = 34.8, height = 22.8, units = "cm", res = 600, pointsize = 12)
  DimPlot(Placebo_Erythropoeitin_harmonised_data, reduction="umap", cols= my_col, pt.size=0.5)
dev.off()
levels(Placebo_Erythropoeitin_harmonised_data)
proportion <- prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$orig.ident), margin = 2)*100

dat <- proportion
dat <- dat[,c(1:6,10,11,12,7,8,9)]
png("Proportion_Pyramidal_subtypes_EPO_PL_samples_V2.png",  width = 16.7, height = 18.8, units = "cm", res = 600, pointsize = 12)
barplot(as.matrix(dat), las=2, col=my_col, space=0.01)
dev.off()   


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

la <- as.numeric(proportion[10,])

wilcox.test(la[c(1,2,3,4,6)], la[c(7,8,10,11,12)])
math =read.table("http://www.utstat.toronto.edu/~brunner/312f12/code_n_data/mathcat.data")
head(proportion)
prop.type <- prop.table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$type), margin = 2)
prop.type
head(table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$type), margin = 2))
head(table(table(Idents(Placebo_Erythropoeitin_harmonised_data), Placebo_Erythropoeitin_harmonised_data$type))
)
apply(prop.type, 2, sum)
dim(Placebo_Erythropoeitin_harmonised_data)
dim(Placebo_Erythropoeitin_harmonised_data$type=="B_samples")
head(Placebo_Erythropoeitin_harmonised_data$type)
dim(Placebo_Erythropoeitin_harmonised_data$type=="B_Samples")
length(Placebo_Erythropoeitin_harmonised_data$type=="B_Samples")
length(Placebo_Erythropoeitin_harmonised_data$type=="A_Samples")
table(Placebo_Erythropoeitin_harmonised_data$celltype)
head(Placebo_Erythropoeitin_harmonised_data$celltypeCondition)
table(Placebo_Erythropoeitin_harmonised_data$celltypeCondition))

fisher.test(df, alternative="two.sided", simulate.p.value=T)
savehistory("modifying_figures_Pyramidal.Rhistory")
