PTEN_codes/01_UMAP.R at main · yurasong/PTEN_codes · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
#######################################################################################
# 01_marker_genes.R
# This script will generate the UMAP of proceeded data, with custom colours.
#######################################################################################

# Library

library(Seurat)
library(dplyr)
library(tidyverse)
library(data.table)
library(ggplot2)
library(scales)

# Proceeded Data

wt1 <- readRDS("WT_PTEN.rds")
pten6w <- readRDS("PTEN_6W.rds")
pten10m <- readRDS("PTEN_10M.rds")

# UMAP for control sample (Fig. 4a)

DimPlot(wt1, reduction = "umap", label = TRUE,
        label.size = 4, repel = T,
        cols=c("BC p63 low" = "#F8766D",
               "BC Nkx3.1" = "#00C1A7",
               "AD" = "#53B400",
               "Ventral" = "#00C094",
               "Lateral" = "#00B6EB",
               "Proximal" = "#FF63B6",
               "BC Pr" = "#B385FF",
               "Intersparced LC" = "#696969")) +
  NoLegend()

# UMAP for PTEN 6W (Fig. 4b)

DimPlot(pten6w, reduction = "umap", label = TRUE,
        label.size = 4, repel = T,
        cols=c("BC p63 high" = "#C49A00",
               "BC Nkx3.1" = "#00C1A7",
               "BC p63 low" = "#F8766D",
               "HY Nkx3.1" = "#FF4500",
               "Ventral" = "#00C094",
               "AD" = "#53B400",
               "BC Hillock" = "#DB8E00",
               "Proximal" = "#FF63B6",
               "HY BC Prox" = "#00A6FF",
               "LC meta" = "#EF67EB",
               "Prolif" = "#B385FF")) +
  NoLegend()

# UMAP for PTEN 10M (Fig. 6a)

DimPlot(pten10m, reduction = "umap", label = TRUE,
        label.size = 4, repel = T,
        cols=c("BC" = "#F8766D",
               "BC Interferon" = "#00C094",
               "HY BC Prox" = "#00A6FF",
               "HY Interferon" = "#C71585",
               "Prox-LC Interferon" = "#53B400",
               "Prox-LC ClassII Antigen" = "#FF63B6",
               "Prox-LC Chemokine" = "#F4A460",
               "Prox-LC Cx3cr1" = "#708090",
               "Pr" = "#B385FF")) +
  NoLegend() +
  xlim(-5, 5) +
  ylim(-10, 8)