---
title: '[RC17]AllCellTypes Plots'
author: "Nina-Lydia Kazakou"
date: "05/03/2022"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Set-up

### Load libraries

```{r message=FALSE, warning=FALSE}
library(SingleCellExperiment)
library(Seurat)
library(tidyverse)
library(Matrix)
library(scales)
library(cowplot)
library(RCurl)
library(scDblFinder)
library(Matrix)
library(ggplot2)
library(edgeR)
library(dplyr)
library(ggsci)  
library(here)
```

### Colour Palette

```{r load_palette}
mypal <- pal_npg("nrc", alpha = 0.7)(10)
mypal2 <-pal_tron("legacy", alpha = 0.7)(7)
mypal3<-pal_lancet("lanonc", alpha = 0.7)(9)
mypal4<-pal_simpsons(palette = c("springfield"), alpha = 0.7)(16)
mypal5 <- pal_rickandmorty(palette = c("schwifty"), alpha = 0.7)(6)
mypal6 <- pal_futurama(palette = c("planetexpress"), alpha = 0.7)(5)
mypal7 <- pal_startrek(palette = c("uniform"), alpha = 0.7)(5)
mycoloursP<- c(mypal, mypal2, mypal3, mypal4)
```

### Load object

```{r}
RC17_norm <- readRDS(here("data", "Processed", "AllCells", "RC17_AllCells_srt.rds"))
```


Here, I will do some additional plots for the individual cluster markers, just to make the FeaturePlots easier to read.

```{r}
Idents(RC17_norm) <- "ClusterID"
```

## Radial Glia

```{r}
radial_glia <- subset(RC17_norm, idents = c("Radial_Glia_1", "Radial_Glia_2", "Radial_Glia_3"))

radial_glia_markers <- c("VIM", "PAX6", "HES1")
```

```{r Radial Glia}
FeaturePlot(radial_glia, radial_glia_markers, pt.size = 0.9, label = FALSE)
```

## Outer-Radial Glia
```{r}
oRG <- subset(RC17_norm, idents = c("Outer-Radial_Glia_1", "Outer-Radial_Glia_2", "Outer-Radial_Glia_3"))

oRG_markers <- c("HOPX", "PTPRZ1")
```


```{r Outer-Radial Glia}
FeaturePlot(oRG, oRG_markers, pt.size = 0.9, label = FALSE)
```

## Radial_Glia/Pre-OPCs
```{r}
pre_OPC <- subset(RC17_norm, idents = c("Radial_Glia/Pre-OPCs_1", "Radial_Glia/Pre-OPCs_2", "Outer-Radial_Glia_3"))

pre_OPC_markers <- c("SPARCL1", "BCAN")
```


```{r Radial_Glia/Pre-OPCs}
FeaturePlot(pre_OPC, pre_OPC_markers, pt.size = 0.9, label = FALSE)
```


## Astrocytes
```{r}
astro <- subset(RC17_norm, idents = c("Astrocytes_1", "Astrocytes_2"))

astro_markers <- c("AQP4", "SPON1", "TAGLN2")
```


```{r Astrocytes}
FeaturePlot(astro, astro_markers, pt.size = 0.9, label = FALSE)
```

## Oligodendroglia
```{r}
oligo <- subset(RC17_norm, idents = c("Oligodendroglia_1", "Oligodendroglia_2", "Oligodendroglia_3", "Oligodendroglia_4", "Oligodendroglia_5", "Oligodendroglia_6"))

oligo_markers <- c("OLIG1", "OLIG2", "SOX10")
```


```{r Oligodendroglia}
FeaturePlot(oligo, oligo_markers, pt.size = 0.9, label = FALSE)
```

## Neurons
```{r}
neuro <- subset(RC17_norm, idents = c("Neurons_1", "Neurons_2", "Neurons_3"))

neuro_markers <- c("DCX", "SOX11", "STMN2")
```


```{r Neurons}
FeaturePlot(neuro, neuro_markers, pt.size = 0.9, label = FALSE)
```


## Pericytes
```{r}
peri <- subset(RC17_norm, idents = c("Pericytes"))

peri_markers <- c("ACTA2", "ANXA2")
```


```{r Pericytes}
FeaturePlot(peri, peri_markers, pt.size = 0.9, label = FALSE)
```


```{r AllCellTypes_ClusterMarkers, fig.height=8, fig.width=12.5}
DotPlot(RC17_norm, features = c(radial_glia_markers, oRG_markers, pre_OPC_markers, astro_markers, oligo_markers, neuro_markers, peri_markers), group.by = "ClusterID") + FontSize(8)
```



```{r}
sessionInfo()
```