Hicat_FindMarkers_FEB23.Rmd

```{r}
#https://data.nemoarchive.org/biccn/grant/u01_devhu/kriegstein/transcriptome/scell/10x_v2/human/processed/analysis/Herb_2022_Hypothalamus/SeuratObj/
library(Seurat)
library(tidyverse)
EdKaZhouHypoNeurons = readRDS("~/Downloads/EdKaZhouHypoNeurons_mt10_integrated.rds")
Meta = read.csv("~/Downloads/HSatlasNeuron_metadata.csv", row.names = 1)
HiCat250 = Meta %>% dplyr::select(HiCat_DE_250)
AdultHypo = subset(EdKaZhouHypoNeurons, cells = row.names(Meta))

AdultHypo = AddMetaData(AdultHypo, HiCat250, "HiCat250")
Idents(AdultHypo) = "HiCat250"
DefaultAssay(AdultHypo) = "RNA"

TFS = read.csv("~/Library/CloudStorage/Box-Box/HG2553 Main Folder/Useful Gene Lists/Human TFs.csv", head=F)
NPS = read.csv("~/Dropbox/Columbia/Claudia Maria Hannah Shared/Punch Bipsies Manuscript/Neuropeptide list - 6MAR20.csv", head=F)

AllTFsNPs = subset(c(TFS$V1, toupper(NPS$V1)), c(TFS$V1, toupper(NPS$V1)) %in% row.names(AdultHypo))


Markers = FindAllMarkers(AdultHypo, logfc.threshold = 0.25, features = AllTFsNPs)
Markers2 = subset(Markers, Markers$p_val_adj < 0.05)
write.csv(Markers, "Hicat_DEGs.csv")

CompileTopMarkers = as.data.frame(matrix(ncol = 5, nrow = 0))
colnames(CompileTopMarkers) = c("Hicat", "Top1", "Top2", "Top3", "Concat")

for(x in unique(Markers2$cluster)){
GetMarkers = subset(Markers2, Markers2$cluster == x)
GetMarkers = GetMarkers[order(-GetMarkers$avg_log2FC), ]

if(dim(GetMarkers)[1] >= 3){
Top3 = head(GetMarkers, 3)
DF = as.data.frame(t(c(x, Top3$gene, paste(Top3$gene, collapse ="/"))))
colnames(DF) = c("Hicat", "Top1", "Top2", "Top3", "Concat")

}else{
NAs = 3- dim(GetMarkers)[1]
DF = as.data.frame(t(c(x, GetMarkers$gene, rep(NA, NAs), paste(GetMarkers$gene, collapse ="/"))))
colnames(DF) = c("Hicat", "Top1", "Top2", "Top3", "Concat")
}
CompileTopMarkers = rbind(CompileTopMarkers, DF)
write.csv(CompileTopMarkers, "~/Downloads/HicatMarkers/HiCatDEGs_Comb.csv")
}
```