---
author: "Hu Zheng"
date: "2024-12-01"
date-format: YYYY-MM-DD
---
# FigureS4
```{r}
#| warning: false
#| message: false
library(Seurat)
library(tidyverse)
library(hdWGCNA)
source('bin/Palettes.R')
```
```{r}
seu.harmony <- readRDS('../data/seu.harmony.rds')
seu.harmony.metadata <- readRDS('../data/seu.harmony.metadata.rds')
seu.harmony@meta.data <- seu.harmony.metadata
seu.IT <- subset(seu.harmony, cells=colnames(seu.harmony)[which(
seu.harmony$SubType %in% names(col_SubType)[1:8]
)])
seu.Ex <- seu.harmony[,seu.harmony$SubType %in% names(col_SubType)[1:11]]
```
```{r}
seurat_obj <- readRDS("../data/Figure4/seu.Ex.hdwgcna.rds")
```
## Figure_S4A
```{r fig.width=8, fig.height=4}
#| message: false
#| warning: false
Figure_S4A <- PlotDendrogram(seurat_obj, main='hdWGCNA Dendrogram')
Figure_S4A
```
```{r}
#| eval: false
ggsave("../../Figure/FigureS4/Figure_S4A.pdf", plot = Figure_S4A,
height = 4, width = 8, units = "in")
```
## Figure_S4B
```{r}
#| eval: false
ModuleNetworkPlot(
seurat_obj,
outdir = '../../Figure/Figure4/ModuleNetwork'
)
```
```{r}
knitr::include_graphics("./images/Figure_S4B.png", dpi = 300)
```
## Figure_S4C
```{r fig.width=6, fig.height=6}
#| message: false
seu <- seu.IT
seu$orig.ident <- factor(seu$orig.ident, levels = c("P1","P4","P10","Adult"))
gene_list <- c("Cdh2","Ncam1","Sema4g","Igsf3","Lrp8")
Figure_S4C <-
VlnPlot(seu, features = rev(gene_list), group.by = "orig.ident", cols=col_Time,
split.by = "orig.ident",
stack = TRUE, flip = TRUE) +
theme(legend.position = "none", axis.text.x = element_text(angle = 0, hjust = 0.5)) +
labs(x="")
Figure_S4C
```
```{r}
#| eval: false
ggsave("../../Figure/FigureS4/Figure_S4C.pdf", plot = Figure_S4C,
height = 6, width = 10, units = "in")
```
## Figure_S4D
```{r fig.width=6, fig.height=6}
#| message: false
seu <- seu.IT
seu$orig.ident <- factor(seu$orig.ident, levels = c("P1","P4","P10","Adult"))
gene_list <- c("Efnb3","Cdh13","Sdc3","Cd200","L1cam")
Figure_S4D <-
VlnPlot(seu, features = gene_list, group.by = "orig.ident", cols=col_Time,
split.by = "orig.ident",
stack = TRUE, flip = TRUE) +
theme(legend.position = "none", axis.text.x = element_text(angle = 0, hjust = 0.5)) +
labs(x="")
Figure_S4D
```
```{r}
#| eval: false
ggsave("../../Figure/FigureS4/Figure_S4D.pdf", plot = Figure_S4D,
height = 6, width = 10, units = "in")
```
