Compare_with_Nestler.Rmd

---
title: "Compare with Nestler"
author: "Mohamed Nadhir Djekidel"
date: "February 7, 2019"
output: html_document
---

# load libraries

```{r}
require(SC2P)
require(readxl)
```


# load our DEG data 

```{r}
load("Excitatory/Excitatory_DEG.RData")
load("inhibitory_DEG.RData")
load("FinalObjects/NonNeuro_DEG.RData")

names(Excitatory_DEG) = paste0("Exc_",names(Excitatory_DEG))
names(inhibitory_DEG) = paste0("Inhib_",names(inhibitory_DEG))

deg_all = c(Excitatory_DEG,inhibitory_DEG,NonNeuro_DEG)
```

# get the list of DEG

```{r}
deg_all_sig = list()

for(cellType in names(deg_all)){
  deg_all_sig[[cellType]] = list()
  for(period in names(deg_all[[cellType]])){
    deg_all_sig[[cellType]][[period]] = list()  
    if(is.data.frame(deg_all[[cellType]][[period]])){
      df1  = topGene(deg_all[[cellType]][[period]],phase = "both",
          number = 30000,p.value = 0.05)
      deg_all_sig[[cellType]][[period]] <-df1 # subset(df1, Phase2 == "Y")
    }
  }
}

```

# load Nestlet DEG data

```{r}
DEG_nestler_C24vS24 <- read_xlsx("../../../Public/Nestler_Cocaine_2018/Table_S1_DEGs.xlsx",sheet = "CCvSS")

DEG_nestler_C24vS24_PFC <- DEG_nestler_C24vS24[,c("PFC","X__1","X__2")]
colnames(DEG_nestler_C24vS24_PFC) = DEG_nestler_C24vS24_PFC[1,]
DEG_nestler_C24vS24_PFC = DEG_nestler_C24vS24_PFC[-1,]

nbovp = matrix(0,nrow=length(deg_all_sig),ncol=3)
colnames(nbovp) = names(deg_all_sig$Exc_1)
rownames(nbovp) = names(deg_all_sig)

for(cellType in names(deg_all_sig)){
  for(period in names(deg_all_sig[[cellType]])){
    if(is.data.frame(deg_all_sig[[cellType]][[period]])){
        nbovp[cellType,period] = length(intersect(as.character(deg_all_sig[[cellType]][[period]]$Gene.name), 
                                                  as.character(DEG_nestler_C24vS24_PFC$GeneID) ))
    }
  }
}
```


# Check the cellular composition of their data

```{r}
require(Seurat)
require(pheatmap)
load("FinalObjects/all_cell_inDD_saline_sobj.RData")

 ae = AverageExpression(all_cell_inDD_saline_sobj)
toUse = intersect(as.character(DEG_nestler_C24vS24_PFC$GeneID),rownames(ae))

ph = log2(ae[toUse,]+1)
```


# Do overlap

```{r}

```