化脓性汗腺炎和银屑病单细胞数据复现2-小提琴图复现

生信菜鸟团

发布于 2024-04-18 19:57:21

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发布于 2024-04-18 19:57:21

文章被收录于专栏：生信菜鸟团生信菜鸟团

上次推文更新了一篇文章复现，今天同样是接着之前那篇文章来做一下小提琴图的复现。上次推文链接：日光性皮炎和银屑病单细胞数据集复现 同时来一个纠错，之前写的日光性皮炎应该是化脓性汗腺炎和 HIS 修改为 HS

library(ggsci)
library(dplyr) 
library(Seurat)
library(cowplot)
library(data.table)
library(dplyr)
library(ggplot2)
library(stringr)
getwd()
sce.all=readRDS("./2-harmony/sce.all_int.rds")

sce.all.int=sce.all
celltype=data.frame(ClusterID=0:18 ,
                    celltype= 0:18) 
#定义细胞亚群        
celltype[celltype$ClusterID %in% c( 2,4,5,7,8,11,12,15,16 ),2]='Keratinocyte'
celltype[celltype$ClusterID %in% c( 13 ),2]='Fibroblast'   
celltype[celltype$ClusterID %in% c( 9 ),2]='DC-2'  
celltype[celltype$ClusterID %in% c( 3 ),2]='DC-1'
celltype[celltype$ClusterID %in% c( 0,1),2]='T'   
celltype[celltype$ClusterID %in% c( 10),2]='melanocytes' 
celltype[celltype$ClusterID %in% c( 17),2]='cycling' 
celltype[celltype$ClusterID %in% c( 14),2]='B'   
celltype[celltype$ClusterID %in% c( 6 ),2]='plasma'    
celltype[celltype$ClusterID %in% c( 18),2]='Mast' 
head(celltype)
celltype
table(celltype$celltype)
sce.all.int@meta.data$celltype = "NA"

for(i in 1:nrow(celltype)){
  sce.all.int@meta.data[which(sce.all.int@meta.data$RNA_snn_res.0.8 == celltype$ClusterID[i]),'celltype'] <- celltype$celltype[i]}
Idents(sce.all.int)=sce.all.int$celltype
table( Idents(sce.all.int))

sel.clust = "celltype"
sce.all.int <- SetIdent(sce.all.int, value = sel.clust)
table(sce.all.int@active.ident) 
p_umap=DimPlot(sce.all.int, reduction = "umap", group.by = "celltype",label = T,label.box = T)
p_umap

p2=VlnPlot(sce.all.int, group.by = "celltype", split.by = "group",features = "IL1B", pt.size = 0, ncol = 3, same.y.lims=T) + 
  scale_y_continuous(breaks=seq(0, 100, 5)) +
  NoLegend()
p2
#修正上次推文的HIS为HS
sce.all.int$group<-ifelse(grepl("GSM6840117|118|119|120|121|122|123|124",sce.all$orig.ident),"HS"            ifelse(grepl("GSM6840143|144|145|146|147|148|149|150|151|152",sce.all$orig.ident),"Control", "Psoriasis"))
table(sce.all.int$group)
#因子改变分组顺序
sce.all.int$group<-factor(sce.all.int$group,levels=c("Control","Psoriasis","HS"))

pp1<-VlnPlot(sce.all.int,group.by = "group", "IL17A")+ theme(axis.text.x=element_text(angle=45,hjust = 1));pp1
pp2<-VlnPlot(sce.all.int,group.by = "group", "IL17F")+ theme(axis.text.x=element_text(angle=45,hjust = 1));pp2
pp3<-VlnPlot(sce.all.int,group.by = "group", "IL23R")+ theme(axis.text.x=element_text(angle=45,hjust = 1));pp3
library(patchwork)
pp1+pp2+pp3+plot_layout(ncol = 3)
ggsave(file="vplot_1.pdf",width = 8,height = 3)

pp<-VlnPlot(sce.all.int,group.by = "group", "IL1B")+ theme(axis.text.x=element_text(angle=45,hjust = 1));pp
pp4<-VlnPlot(sce.all.int,group.by = "celltype", split.by = "group", "IL1B")+
  theme(axis.text.x=element_text(angle=45,hjust = 1));pp4
ggsave(file="vplot_2.pdf",width = 10,height = 3)