suppressPackageStartupMessages({
library(Seurat)
library(stringr)
library(sctransform)
library(future)
require(scales)
library(RColorBrewer)
library("readxl")
library(dplyr)
library(dendextend)
})
### figure 2 + supplements
# import the Dopaminergic nuclei (mDA) dataset.
sobj <- readRDS("/path/to/dir/mDA.rds")
# Figure 2 UMAP
p <- DimPlot(sobj, group.by = "kmeans71", cols = c("3"="#B35806", "56"="#B35806", "12"="#2171B5", "26"="#2171B5", "54"="#2171B5",
"65"="#2171B5", "40"="#2171B5", "13"="#2171B5", "20"="#2171B5", "52"="#2171B5",
"17"="#2171B5", "28"="#2171B5", "27"="#2171B5", "45"="#2171B5", "33"="#2171B5",
"23"="#2171B5", "29"="#2171B5", "66"="#2171B5", "9"="#2171B5", "67"="#2171B5",
"31"="#2171B5", "44"="#2171B5", "22"="#2171B5", "46"="#2171B5", "14"="#2171B5",
"11"="#2171B5","30"="#2171B5", "1"="#2171B5", "38"="#2171B5", "41"="#2171B5",
"61"="#2171B5", "21"="#2171B5", "50"="#2171B5", "19"="#2171B5", "42"="#2171B5",
"4"="#2171B5", "10"="#2171B5", "2"="#2171B5", "39"="#2171B5", "60"="#2171B5",
"5"="#2171B5", "43"="#2171B5", "37"="#2171B5", "53"="#2171B5", "15"="#00441B",
"71"="#00441B", "49"="#00441B", "68"="#00441B", "8"="#DF65B0", "62"="#DF65B0",
"58"="#DF65B0", "47"="#DF65B0", "55"="#DF65B0", "16"="#DF65B0", "63"="#DF65B0",
"6"="#DF65B0", "7"="#DF65B0", "24"="#DF65B0", "18"="#FB9A99", "57"="#FB9A99",
"69"="#FB9A99", "48"="#FB9A99", "59"="#FB9A99", "70"="#FB9A99", "25"="#FB9A99",
"34"="#FB9A99", "32"="#FB9A99", "64"="#FB9A99", "51"="#969696", "35"="#969696",
"36"="#969696")) + coord_fixed() + NoLegend()
tiff(file = "/path/to/dir/plot_name.tiff",
units="cm", width=25, height=25, res=300)
LabelClusters(plot = p, id = 'kmeans71', color = 'white', size=4, fontface = 'bold', box = T, max.overlapp = Inf, repel=T)
dev.off()
# Figure 2 dendrogram
dend <- as.dendrogram(hc71)
tiff(file = "/path/to/dir/plot_name.tiff",
units="cm", width=18, height=2, res=300)
p1 <- dend %>% set("leaves_pch", 15) %>%
set("leaves_cex", 0.01) %>%
set("branches_lwd", 0.4) %>%
set("leaves_col", c("3"="#B35806", "56"="#B35806", "12"="#2171B5", "26"="#2171B5", "54"="#2171B5",
"65"="#2171B5", "40"="#2171B5", "13"="#2171B5", "20"="#2171B5", "52"="#2171B5",
"17"="#2171B5", "28"="#2171B5", "27"="#2171B5", "45"="#2171B5", "33"="#2171B5",
"23"="#2171B5", "29"="#2171B5", "66"="#2171B5", "9"="#2171B5", "67"="#2171B5",
"31"="#2171B5", "44"="#2171B5", "22"="#2171B5", "46"="#2171B5", "51"="#969696",
"14"="#2171B5", "11"="#2171B5","30"="#2171B5", "1"="#2171B5", "38"="#2171B5",
"41"="#2171B5", "61"="#2171B5", "21"="#2171B5", "50"="#2171B5", "19"="#2171B5",
"42"="#2171B5", "4"="#2171B5", "10"="#2171B5", "2"="#2171B5", "39"="#2171B5",
"60"="#2171B5", "5"="#2171B5", "43"="#2171B5", "37"="#2171B5", "53"="#2171B5",
"8"="#DF65B0", "62"="#DF65B0", "15"="#00441B", "71"="#00441B", "49"="#00441B",
"68"="#00441B", "47"="#DF65B0", "55"="#DF65B0", "16"="#DF65B0", "63"="#DF65B0",
"36"="#969696", "35"="#969696", "6"="#DF65B0", "7"="#DF65B0", "24"="#DF65B0",
"18"="#FB9A99", "57"="#FB9A99", "69"="#FB9A99", "48"="#FB9A99", "59"="#FB9A99",
"58"="#DF65B0", "70"="#FB9A99", "25"="#FB9A99", "34"="#FB9A99", "32"="#FB9A99",
"64"="#FB9A99"))
ggplot(p1, labels = F)
dev.off()
# Figure 2 dotplot
my.levels <- as.character(hc71$order)
# re-order levels according to dendrogram leaf nodes
sobj$kmeans71 <- factor(x = sobj$kmeans71 , levels = my.levels)
markers <- rev(unique(c("Mog", "Mag", 'Th', 'Slc6a3', 'Ddc', 'En1', 'Nr4a2', 'Pitx3',
"Prlr", 'Satb2', "Slc17a7", "Slc17a6", "Gad1", "Gad2", "Slc32a1")))
tiff(file = "/path/to/dir/plot_name.tiff",
units="cm", width=55, height=20, res=300)
DotPlot(sobj, assay = "RNA", features = markers, group.by = "kmeans71") + coord_flip() +
theme(axis.text.x = element_text(size = 13, face = "bold", angle = 0, hjust = 0.5, vjust = 0.5),
axis.text.y = element_text(size = 18, face = "bold", angle = 0))
dev.off()
sessionInfo()