library(Seurat)
library(dplyr)

Full_final <- readRDS("/DATA/31/molteni/vexas_mouse_4/results/Full/01-seurat/Full_final.rds")

# #########################################################################################################################
# # computation on custom annotation
# 

Full_final <- readRDS("/DATA/31/molteni/vexas_mouse_4/results/Full/01-seurat/Full_final_annot.rds")

setwd("/DATA/31/molteni/vexas_mouse_4/results/DE_markers/AvsB/")

clusters <- unique(Full_final@meta.data$celltypes_annot)

for(i in clusters) {
  markers <- FindMarkers(Full_final, ident.1 = "Pool_A_m", group.by = "orig.ident", subset.ident = i)
  markers['cluster'] <- i
  filename=paste("markers_cluster_",i,".csv", sep="")
  write.csv(markers, file=filename)
}

df <- list.files(path="/DATA/31/molteni/vexas_mouse_4/results/DE_markers/AvsB") %>% 
  lapply(read.csv) %>% 
  bind_rows

df <- df[df$p_val_adj<0.05,]

setwd("/DATA/31/molteni/vexas_mouse_4/results/summary/")
write.csv(df, file="PoolA_mvsPoolB_m_sigMarkers.csv")
cells_by_sample <- table(Full_final@meta.data$celltypes_annot, Full_final@meta.data$orig.ident)
write.csv(cells_by_sample, file="cells_bysample.csv")

cc_distribution <-as.data.frame (table(Full_final$Phase, Full_final$orig.ident, Full_final$celltypes_annot))
colnames(cc_distribution) <- c("Phase","orig.ident","cluster","CellNumb")
write.csv(cc_distribution, file="cell_cycle.csv")