Seurat 提取亚细胞群并画出给定基因列表的Dotplot图

Seurat 提取亚细胞群并画出给定基因列表的Dotplot图

代码如下：

library(SeuratDisk)
library(patchwork)
library(dplyr)
library(Seurat)

hv1 <- readRDS(file = "./singlecell/bairong/fastgenomics-Hv1h5ad_2000vf-202304231117.rds")
# hv1_3 <- readRDS(file = "./singlecell/bairong/fastg-hv1-subcells_202308081058.rds")

hv1
# 28527 features across 584884 samples within 1 assay 
# 2 dimensional reductions calculated: scanvi_emb, umap

head(hv1@meta.data$anatomical_region_level_1)
# [1] parenchyma parenchyma parenchyma airway     airway     airway    
# Levels: airway nose parenchyma

table(hv1@meta.data$anatomical_region_level_1)
# airway       nose parenchyma 
# 173194      78279     333411 


# 需要提取一下细胞群作为亚群
sub_class = c("Basal resting","Suprabasal","Multiciliated (nasal)",
              "Multiciliated (nasal)","Multiciliated (non-nasal)",
              "Club (non-nasal)","Club (nasal)","Goblet (nasal)",
              "Goblet (bronchial)","Goblet (subsegmental)","AT1","AT2",
              "AT2 proliferating")


# hv1_finest_sub 亚群提取 到hv1_fs 
hv1_fs = hv1[,hv1@meta.data$ann_finest_level %in% sub_class]


# 需要展示的基因名
Proteases = c("MMP1","CTSL","TMPRSS2","IHH","IMMP2L","ZFYVE9","\
NAALADL2","USP39","TMPRSS11E","MMP2","PRSS22","MMP15","ECE2","PRSS35","\
RNF128","ADAMTS4","ADAM33","CAPN13","USP47","CAPN11","KLK5","AGTPBP1","\
TINAGL1","ADAMTS12","PSMB9","USP29","ASPRV1","CNDP1","DNPEP","PSMB1","CTSE","\
RNF13","PSMA1","CELA1")

# 保存亚群
#saveRDS(hv1_fs, file = "./singlecell/bairong/fastg-hv1-subcells_202308081058.rds",compress = F)#快

# Test用
# Proteases = c("ADAM33")

# 作点图 轴翻转，基因名为纵坐标
DotPlot(hv1_fs, features = Proteases, group.by="ann_finest_level" ,        
        dot.min = 0,
        dot.scale = 4,
        col.min=-2.5, col.max=2.5,
        scale.min = 0,
        scale.max = 40,
        cols = c("yellow","red"))+  RotatedAxis()+coord_flip()


DotPlot(hv1_fs, features = Proteases, group.by="ann_finest_level" ,        
        dot.min = 0,
        dot.scale = 4,
        col.min=-2.5, col.max=2.5,
        scale.min = 0,
        scale.max = 0.1,
        cols = c("yellow","red"))+  RotatedAxis()


hv1@meta.data$ann_finest_level
hv1_3@meta.data$ann_finest_level

scale.min max影响圆圈显示大小 上下限
cols = c("yellow","red") 颜色由黄到红