---
title: "09_Marker_gene_expr_test"
author: "Luise A. Seeker"
date: "05/02/2021"
output: html_document
---
```{r}
library(Seurat)
library(ggplot2)
library(ggsci)
library("scales")
library(RCurl)
library(AnnotationHub)
```
Pick colour paletts
```{r}
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, mypal5, mypal6, mypal7)
show_col(mycoloursP, labels =F)
```
```{r}
seur_comb <- readRDS("/Users/lseeker/Documents/Work/HumanCellAtlas/splice_control_out/datasets/04_scran_normalised/combined_SCE/combined_seur_norm_raw.RDS")
```
Neurons:
```{r, fig.width=7, fig.height=5, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("SNAP25", "STMN2", "RBFOX3", "GABRB2"))
```
Inhibitory neurons
```{r, fig.width=7, fig.height=5, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("GAD1", "GAD2", "SLC32A1", "PVALB"))
```
Add inhibitory neurons
```{r, fig.width=7, fig.height=5, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("ADARB2", "VIP", "LAMP5", "LHX6"))
```
Add 2 Inhibitory Neurons
```{r, fig.width=7, fig.height=23, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("LAMA3", "VIP", "TAC3", "RYR3", "TSHZ2",
"RELN", "IL1RAPL2", "CXCL14", "EYA4",
"FBXL7", "KIT", "MEIS2", "PBX3", "PLCL1",
"MYO5B", "TRHDE", "PLCH1"),
ncol = 2)
```
Excitatory neurons
```{r, fig.width=7, fig.height=5, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("SATB2", "SLC12A6", "SLC17A7"))
```
Add exitatory neurons:
```{r, fig.width=7, fig.height=5, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("FEZF2",
"RORB",
"THEMIS"))
```
Astrocytes
```{r, fig.width=7, fig.height=15, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("GJA1",
"AQP4",
"GLUL",
"SOX9",
"NDRG2",
"GFAP",
"ALDH1A1",
"ALDH1L1",
"VIM",
"APOE",
"FGFR3"),
ncol = 2)
```
Add Astrocytes
```{r, fig.width=7, fig.height=35, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c( "HPSE2",
"TENM2",
"ZNF98",
"CCDC85A",
"SLC38A1",
"GALNT15",
"BNC2",
"CFAP299",
"SPAG17",
"DTHD1",
"ADGB",
"UAP1",
"SPOCD1",
"CLCF1",
"CDH19",
"SORCS1",
"SAMHD1",
"NRGN",
"CAMK2A",
"THY1",
"ENC1",
"SYT1",
"CALM3",
"ST18",
"CTNNA3",
"APLNR"))
```
Astrocyte markers as described in Zeisel et al. 2018 in the mouse
for telencephalon and non-telencephalon astrocytes
```{r, fig.width=7, fig.height=13, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c( "AGT",
"MFGE8",
"SLC6A11",
"SLC6A9",
"GDF10",
"ISLR",
"GFAP",
"AQP4"))
```
Endothelial cells and pericytes
```{r, fig.width=7, fig.height=10, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c( "CLDN5",
"ICAM2",
"PDGFRB",
"NOTCH3",
"VWF",
"FLT1",
"MECOM"),
ncol = 2)
```
Stromal
```{r, fig.width=7, fig.height=8, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c( "LAMB1" ,
"HSPG2",
"COL4A1",
"FN1",
"LAMA2"),
ncol = 2)
```
Microglia and macrophages
```{r, fig.width=7, fig.height=13, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c( "CD74",
"SPI1",
"MRC1",
"TMEM119",
"CX3CR1",
"AIF1",
"P2RY12",
"C1QC",
"C1QA"),
ncol = 2)
```
Add microglia & macrophages
```{r, fig.width=7, fig.height=13, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("IPCEF1",
"NAV3",
"NAMPT",
"FOSL2",
"IPCEF1",
"NAV3",
"IL1RAPL1",
"FRMD5",
"MAGI2"),
ncol = 2)
```
OPCs
```{r, fig.width=7, fig.height=13, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("PDGFRA",
"CSPG4",
"GPR17",
"PTPRZ1",
"OLIG1",
"OLIG2",
"PCDH15",
"PTGDS",
"BCAN"),
ncol = 2)
```
Add OPC:
```{r, fig.width=7, fig.height=5, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("CABLES1",
"GFRA1",
"LINC01965"),
ncol = 2)
```
Add COP:
```{r, fig.width=7, fig.height=18, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("ETV1",
"CHST9",
"MYT1",
"TENM2",
"CAMK2A",
"KCNQ5",
"SEMA5B",
"SYT1",
"GPR17",
"BMPER",
"EPHB1",
"ARHGAP24",
"DOCK8",
"APBB1IP"),
ncol = 2)
```
Oligodendrocytes
```{r, fig.width=7, fig.height=10, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("PLP1",
"CNP",
"MAG",
"MOG",
"MOBP",
"MBP",
"SOX10" ),
ncol = 2)
```
Additional oligodendrocytes
```{r, fig.width=7, fig.height=18, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("SNAP25",
"CNTN1",
"FRY",
"PLXDC2",
"DYSF",
"PTPRM",
"FOS",
"VIM",
"JUNB",
"AFF3",
"KANK4",
"FSTL5",
"SGCZ",
"MDGA2"),
ncol = 2)
```
```{r, fig.width=12, fig.height=30, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("SNAP25",
"STMN2",
"RBFOX3",
"GABRB2",
"GAD1",
"GAD2",
"SLC32A1",
"SATB2",
"SLC12A6",
"SLC17A7",
"GJA1",
"AQP4",
"GLUL",
"SOX9",
"NDRG2",
"GFAP",
"ALDH1A1",
"ALDH1L1",
"VIM",
"CLDN5",
"VTN",
"ICAM2",
"PDGFRB",
"NOTCH3",
"CD74",
"SPI1",
"MRC1",
"TMEM119",
"CX3CR1",
"AIF1",
"PDGFRA",
"CSPG4",
"GPR17",
"PTPRZ1",
"OLIG1",
"OLIG2",
"PCDH15",
"PTGDS",
"PLP1",
"CNP",
"MAG",
"MOG",
"MOBP",
"MBP",
"SOX10"),
ncol = 4)
```
```{r, fig.width=12, fig.height=12, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("SNAP25",
"GABRB2",
"GJA1",
"AQP4",
"CLDN5",
"ICAM2",
"PDGFRB",
"NOTCH3",
"CD74",
"AIF1",
"PDGFRA",
"CSPG4",
"GPR17",
"PTPRZ1",
"PLP1",
"CNP"),
ncol = 4)
```
```{r, fig.width=8, fig.height=6, fig.fullwidth=TRUE}
DimPlot(seur_comb, label = T, cols = mycoloursP)
```
Look for markers previously found interesting in our analyses:
```{r, fig.width=12, fig.height=12, fig.fullwidth=TRUE}
FeaturePlot(seur_comb, features = c("RBFOX1",
"SPARC",
"OPALIN",
"PAX3",
"NELL1",
"KLK6"))
```