---
title: "HOX genes"
author: "Luise A. Seeker"
date: "19/10/2021"
output: html_document
---
# Load libraries
```{r}
library(Seurat)
library(here)
library(ggsci)
library(dplyr)
```
```{r, echo = F}
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)
```
```{r}
nad_ol <- readRDS(here("data",
"single_nuc_data",
"oligodendroglia",
"srt_oligos_and_opcs_LS.RDS"))
```
```{r}
hox_genes <- c("HOXA1",
"HOXA2",
"HOXA3",
"HOXA4",
"HOXA5",
"HOXA6",
"HOXA7",
"HOXA9",
"HOXA10",
"HOXA11",
"HOXA13",
"HOXB1",
"HOXB2",
"HOXB3",
"HOXB4",
"HOXB5",
"HOXB6",
"HOXB7",
"HOXB8",
"HOXB9",
"HOXB13",
"HOXC4",
"HOXC5",
"HOXC6",
"HOXC8",
"HOXC9",
"HOXC10",
"HOXC11",
"HOXC12",
"HOXC13",
"HOTAIRM1")
```
```{r, fig.width = 9, fig.height = 9}
FeaturePlot(nad_ol, features = c(#"HOXA1",
"HOXA2", "HOXA3", #"HOXA4", "HOXA5",
#"HOXA6",
"HOXA7" #, "HOXA9", "HOXA10", "HOXA11",
#"HOXA13"
),
split.by = "Tissue")
```
```{r, fig.width = 9, fig.height = 6}
FeaturePlot(nad_ol, features = c(#"HOXB1",
"HOXB2",
"HOXB3"
#"HOXB4",
#"HOXB5",
#"HOXB6", "HOXB7", "HOXB8"#,
#"HOXB9", "HOXB13"
),
split.by = "Tissue")
```
```{r}
VlnPlot(nad_ol, feature = "HOXB3", split.by = "Tissue")
```
```{r, fig.width = 9, fig.height = 3}
FeaturePlot(nad_ol, features = c("HOXC4" #, "HOXC5", "HOXC6", "HOXC8", "HOXC9",
#"HOXC10", "HOXC11", "HOXC12", "HOXC13"
),
split.by = "Tissue")
```
```{r, fig.width = 9, fig.height = 3}
VlnPlot(nad_ol, features = c("HOXC4" #, "HOXC5", "HOXC6", "HOXC8", "HOXC9",
#"HOXC10", "HOXC11", "HOXC12", "HOXC13"
),
split.by = "Tissue")
```
```{r, fig.width = 9, fig.height = 6}
FeaturePlot(nad_ol, features = c("HOXD1", "HOXD3" #, #"HOXD4",
#"HOXD8" #, "HOXD9",
#"HOXD10", "HOXD11", "HOXD12", "HOXD13"
),
split.by = "Tissue")
```
```{r, fig.width = 9, fig.height = 6}
VlnPlot(nad_ol, features = c("HOXD1", "HOXD3" #, #"HOXD4",
#"HOXD8" #, "HOXD9",
#"HOXD10", "HOXD11", "HOXD12", "HOXD13"
),
split.by = "Tissue",
ncol = 1)
```
```{r, fig.width = 9, fig.height = 3}
FeaturePlot(nad_ol, features = "HOTAIRM1", split.by = "Tissue")
```
```{r}
VlnPlot(nad_ol, features = "HOTAIRM1", split.by = "Tissue")
```
```{r}
VlnPlot(nad_ol, features = hox_genes, split.by = "Tissue", ncol = 1)
```
Find markers for tissues without setting any thresholds to see if HOX genes
are present in lists
They are not.
```{r, eval=FALSE}
Idents(nad_ol) <- "Tissue"
all_mark <- FindAllMarkers(nad_ol, test.use = "MAST")
```
# Hox gene expression in astrocytes
```{r}
astro_srt<- readRDS(here("data",
"single_nuc_data",
"astrocytes",
"HCA_astrocytes.RDS"))
```
```{r}
astro_srt$astrocytes_clu <- factor(astro_srt$astrocytes_clu, levels = c("AS_1",
"AS_2",
"AS_3",
"AS_4",
"AS_5",
"AS_6",
"AS_7",
"AS_8",
"AS_9",
"AS_10",
"AS_11",
"AS_12",
"AS_13"))
Idents(astro_srt) <- "astrocytes_clu"
```
```{r, fig.width = 8, fig.height = 20}
fil_hox <- subset(hox_genes, hox_genes %in% rownames(astro_srt))
VlnPlot(astro_srt, features = fil_hox, split.by = "Tissue", ncol = 1)
```
session info
```{r}
sessionInfo()
```