---
author: "Hu Zheng"
date: "2024-12-01"
date-format: YYYY-MM-DD
---
# FigureS1
```{r}
#| warning: false
#| message: false
library(Seurat)
library(tidyverse)
library(aplot)
source('bin/Palettes.R')
```
```{r}
#| warning: false
#| message: false
seu.harmony <- readRDS('../data/seu.harmony.rds')
seu.harmony.metadata <- readRDS('../data/seu.harmony.metadata.rds')
seu.harmony@meta.data <- seu.harmony.metadata
```
## Figure_S1A
```{r fig.width=18, fig.height=6}
seu <- seu.harmony
seu$SubType <- factor(seu$SubType, levels = names(col_SubType))
seu$orig.ident <- factor(seu$orig.ident, levels = c("P1","P4","P10","Adult"))
Figure_S1A <-
DimPlot(seu,
reduction = 'umap', group.by = "SubType", label = F, split.by = 'orig.ident',
ncol = 4, cols = col_SubType) +
theme(axis.line = element_blank(), axis.ticks = element_blank(),
axis.text = element_blank(), plot.title = element_text(size = 30)) +
labs(x='', y='', title = "") +
coord_fixed()
Figure_S1A
```
```{r}
#| eval: false
ggsave("../../Figure/FigureS1/Figure_S1A.pdf", plot = Figure_S1A,
height = 6, width = 18, units = "in")
```
## Figure_S1B
```{r fig.width=14, fig.height=8}
#| message: false
# cell type
df_type <- data.frame(
'SubType' = names(col_SubType),
'Color' = as.character(col_SubType)
)
df_type$SubType <- factor(df_type$SubType, levels=names(col_SubType))
p1 <- ggplot(df_type, aes(x=SubType, y=1, fill=SubType)) +
geom_tile() +
scale_fill_manual(values = col_SubType, name="Cell Type") +
theme_void() +
NoLegend()
# dot plot
seu <- seu.harmony
seu$SubType <- factor(seu$SubType, levels = names(col_SubType))
Idents(seu) <- 'SubType'
p2 <- DotPlot(
seu,
features = c('Sox11','Cd24a','Cux2','Calb1','Rorb','Deptor','Oprk1','Pou3f1',
'Npr3','Tshz2','Syt6',
'Lamp5','Pvalb','Sst','Vip',
'Top2a','Gja1','Flt1','C1qc','Ptgds','Pdgfra'),
group.by = 'SubType',
col.min=0, col.max=2, dot.scale = 8) +
coord_flip() +
scale_x_discrete(limits=rev) +
scale_color_gradientn(colours = c("lightblue3", "lightblue", "white", "red", "red4")) +
theme_minimal() +
theme(axis.text.x = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank())
# cell prob
df <- seu.harmony@meta.data[,c("orig.ident","SubType")]
df <- as.data.frame.array(table(df$orig.ident, df$SubType))
df_long <- as.data.frame(apply(df, 2, function(x){x/sum(x)}))
df_long$Time <- rownames(df_long)
df_long <- pivot_longer(df_long, !Time, names_to = "Subtype", values_to = "Prob")
df_long$Time <- factor(df_long$Time, levels = rev(c("P1","P4","P10","Adult")))
p3 <-
ggplot(df_long, aes(x = Subtype, y = Prob, fill = Time)) +
geom_bar(stat = "identity", width = 1) +
scale_fill_manual(values = col_Time) +
labs(x='', y='', title='') +
theme_minimal(base_size = 15) +
theme(panel.grid = element_blank(), plot.title = element_text(hjust = 0.5),
legend.position = "none",
legend.title = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1))
Figure_S1B <-
p2 %>%
insert_top(p1, height = 0.02) %>%
insert_bottom(p3, height = 0.3)
Figure_S1B
```
```{r}
#| eval: false
ggsave("../../Figure/FigureS1/Figure_S1B.pdf", plot = Figure_S1B,
height = 8, width = 14, units = "in")
```
## Figure_S1C
```{r fig.width=6, fig.height=6}
#| message: false
seu <- subset(
seu.harmony,
cells = colnames(seu.harmony)[seu.harmony$SubType %in% names(col_SubType)[1:8]])
seu$SubType <- factor(seu$SubType, levels = names(col_SubType)[1:8])
gene_list <- c("Cd24a","Slc17a7","Cux2","Rorb","Etv1","Npy")
Figure_S1C <-
VlnPlot(seu, features = gene_list, group.by = "SubType", fill.by ="ident",
cols = as.character(col_SubType[1:8]),
stack = TRUE, flip = TRUE) +
theme(legend.position = "none", axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
labs(x="")
Figure_S1C
```
```{r}
#| eval: false
ggsave("../../Figure/FigureS1/Figure_S1C.pdf", plot = Figure_S1C,
height = 6.5, width = 10, units = "in")
```
## Figure_S1D
```{r}
knitr::include_graphics("./images/Figure_S1D.jpg", dpi = 300)
```
## Figure_S1E
```{r fig.width=5, fig.height=5}
column <- c("x_rotated","y_rotated","Im.L2.3.IT","Im.L4.5.IT","Im.L5.IT","Im.L6.IT","L2.3.IT","L4.5.IT","L5.IT","L6.IT","L5.PT","L5.NP","L6.CT","Lamp5","Pvalb","Sst","Vip","NPC","Astro","Endo","Microglia","Oligo","OPC")
P1_cell2loc <- read.csv("../data/Figure1/P1_cell2location.csv", row.names = 1)
P1_cell2loc <- P1_cell2loc[,column]
colnames(P1_cell2loc) <- c("x_rotated","y_rotated",names(col_SubType))
P1_cell2loc$SubType <- as.character(apply(P1_cell2loc[,names(col_SubType)], 1, function(x){
names(which.max(x))
}))
data <- P1_cell2loc
plist <- list()
for (i in 1:length(col_SubType)){
subtype_i <- names(col_SubType)[i]
df_i <- data.frame(
x = data$x_rotated,
y = data$y_rotated,
col = data[,subtype_i]
)
#df_i$col[!data$SubType==subtype_i] <- 0
df_i$col[df_i$col>1] <- 1
df_i$col[df_i$col<0.05] <- 0
plist[[i]] <-
ggplot(df_i, aes(x=x, y=y, color=col)) +
geom_point(size=2) +
scale_color_gradient(low = "#f7f7f7", high=col_SubType[i],
na.value = "#f7f7f7",
limits = c(0,max(df_i$col)),
#limits = c(0,1),
breaks = c(0,max(df_i$col))) +
coord_fixed() +
theme_void() +
theme(legend.position = "none")
subtype_i <- gsub("/","",subtype_i)
#ggsave(paste("../../Figure/Figure1/Figure_1H/",i,".P1_",subtype_i,".png",sep=""),
# plot = plist[[i]], height = 5, width = 5, units = "in")
}
plist[[10]]
```
## Figure_S1F
```{r fig.width=5, fig.height=5}
column <- c("x_rotated","y_rotated","Im.L2.3.IT","Im.L4.5.IT","Im.L5.IT","Im.L6.IT","L2.3.IT","L4.5.IT","L5.IT","L6.IT","L5.PT","L5.NP","L6.CT","Lamp5","Pvalb","Sst","Vip","NPC","Astro","Endo","Microglia","Oligo","OPC")
P77_cell2loc <- read.csv("../data/Figure1/P77_cell2location.csv", row.names = 1)
P77_cell2loc <- P77_cell2loc[,column]
colnames(P77_cell2loc) <- c("x_rotated","y_rotated",names(col_SubType))
P77_cell2loc$SubType <- as.character(apply(P77_cell2loc[,names(col_SubType)], 1, function(x){
names(which.max(x))
}))
data <- P77_cell2loc
plist <- list()
for (i in 1:length(col_SubType)){
subtype_i <- names(col_SubType)[i]
df_i <- data.frame(
x = data$x_rotated,
y = data$y_rotated,
col = data[,subtype_i]
)
#df_i$col[!data$SubType==subtype_i] <- 0
df_i$col[df_i$col>1] <- 1
df_i$col[df_i$col<0.05] <- 0
plist[[i]] <-
ggplot(df_i, aes(x=x, y=y, color=col)) +
geom_point(size=0.8) +
scale_color_gradient(low = "#f7f7f7", high=col_SubType[i],
na.value = "#f7f7f7",
limits = c(0,max(df_i$col)),
breaks = c(0,max(df_i$col))) +
coord_fixed() +
theme_void() +
theme(legend.position = "none")
subtype_i <- gsub("/","",subtype_i)
#ggsave(paste("../../Figure/Figure1/Figure_1J/",i,".P77_",subtype_i,".png",sep=""),
# plot = plist[[i]], height = 5, width = 5, units = "in")
}
plist[[10]]
```
