单细胞免疫细胞基因marker Marker Gene List
gene.list =c("CD3D",'CD3E','CD2',
'COL1A1','DCN','C1R',
'LYZ','CD68','TYROBP',
'CD79A','MZB1','MS4A1',
'CLDN5','FLT1','RAMP2',
'CPA3','TPSAB1','TPSB2',
'LILRA4','CXCR3','IRF7')
留学申请中介gene.list = c('LEF1','TCF7','SELL',
'IL7R','CD40LG','ANXA1','FOS','JUN',
'FOXP3','SAT1','IL2RA','CTLA4',
'PDCD1','CXCL13','CD200','TNFRSF18',
'CCR7','NELL2','CD55','KLF2',
'TOB1',
'GZMK','EOMES','ITM2C',
'GZMH',
'GZMB','LAG3','CCL4L2','CCL5',
'FCGR3A','FGFBP2','TYROBP','CX3CR1',
'AREG','XCL1','KLRC1','GNLY','KLRD1',
'TRDV2','TRGV9','MTRNR2L8',
'TRDV1','KLRC3','CTSW','CD7',
'MK167','STMN1','TUBA1B','HIST1H4C')
CD4.naive.marker = c('LEF1','TCF7','SELL')
marker = c('IL7R','CD40LG','ANXA1','FOS','JUN')
CD4.Trg.Reg.marker = c('FOXP3','SAT1','IL2RA','CTLA4')
CD8.naive.marker = c('CCR7','NELL2','CD55','KLF2')
marker = c('GZMK','EOMES','ITM2C')
Gama.marker = c('TRDV2','TRGV9','MTRNR2L8')
Semi.marker = c('TRDV1','KLRC3','CTSW','CD7')
Pro.marker = c('MK167','STMN1','TUBA1B','HIST1H4C')
# PBMC Marker
包括T细胞（CD3D，CD3E，CD3G，60.00％）
CD4 + T细胞（CD4，36.94％）
- Th1 细胞属于CD4 细胞属，（INF-γ）
CD8 + T细胞（CD8A , CD8B , 18.53%)
⾃然杀伤 (NK) 细胞 (NCAM1或CD56，KLRB1，NKG7，5.44％）
B细胞（CD19，MS4A1或CD20，CD38，22.27％）
单核细胞（CD14，CD68，FCGR3A或CD16，9.60％）
髓样树突状细胞（mDC的）（CD1C， 0.26%)
浆细胞样树突细胞 (pDCs) ( LILRA4 , 0.18%)
和造⾎⼲细胞和祖细胞 (HSPCs) ( CD34 , 0.12%)
红细胞（HBB，0.99%）
巨核细胞（PPBP）, 0.92%)
Cell Annotion
### Cell Markers
mushrooms
provided
### Define CellType
cell_type = ls() %>% grep('marker',.,value = T) %>% gsub('\\.marker','',.)
markers = ls() %>% grep('marker',.,value = T)
#cell_type = c('T-cell','Fibroblast','Myeloid cell','Cancer cell','B-cell','Endothelial cell','Mast cell',"pDC")
#markers = c("T.cell.marker","ll.marker","ll.marker","ll.marker", "B.cell.marker","ll.marker", "ll.marker","DC. cell.marker")
新加坡国立大学学费
for(i in1:length(cell_type)){
p = DotPlot(sce, features = get(markers[i])) + coord_flip()
ids = as.numeric(p$data[which(p$p.scaled >0),]$id)-1
ids = table(ids)[which(table(ids)>=2)] %>% names() %>% as.numeric()
ids = rownames(sce@meta.data[which(sce@meta.data$urat_clusters %in% ids),])
assign(cell_type[i], ids)
}
# Cell types were preliminarily identified according to expression levels
i padrest = tdiff(rownames(sce@meta.data),ids)
ids = NULL
for(i in cell_type){很爱很爱你日语版
ids = paste0(ids,'ifel(rownames(sce@meta.data) %in% get(\'',i,'\'),\'',i,'\',')
}
ids = paste0(ids,"\'rest\'",str_c(rep(')',length(cell_type)),collap=''))公主日记2片尾曲
sce@meta.data$cell_annotion= eval(par(text = ids))
### Check Unique & consistency
check.unique = NULL
for(i in1:7){
for(j in(i+1):8){
len = interct(get(cell_type[i]),get(cell_type[j]))
if(length(len)!=0){
ids = c(cell_type[i],cell_type[j],markers[i],markers[j],length(len))
check.unique = rbind(check.unique,ids)
}
}
}
check.unique
英语名言佳句
> Manual Adjusti=5# for i in 1:dim(check.unique)[1]
ids1 = check.unique[i,1]
ids2 = check.unique[i,2]
gen1 = check.unique[i,3]
gen2 = check.unique[i,4]
ids = interct(get(ids1),get(ids2))
DotPlot(sce[,ids], features = c(get(gen1),get(gen2))) + coord_flip()
ids1
ids2
ids = sce@meta.data[which(sce@meta.data$urat_clusters==8),] %>% rownames()
DotPlot(sce[,ids], features =gene.list) + coord_flip()
DotPlot(sce[,rest], features =gene.list) + coord_flip()
sce@meta.data[which(sce$urat_clusters==19),'cell_annotion']="T-cell"
> consistencysce@meta.data$cell_annotion= str_replace_all(sce@meta.data$cell_annotion, c("B-cell"="B_cell",
"Cancer cell"="Cancer_cell",
"Endothelial cell"="Endothelial_cell",
"Fibroblast"="Fibroblast",
"Mast cell"="Mast_cell",
"Myeloid cell"="Myeloid_cell",
"pDC"="pDC",
"T-cell"="T_cell"))
### plot
p1 = DimPlot(sce,reduction ="tsne",label=T, group.by ="cell_annotion",cols=mycolors[6:15],label.size=2.5) p2 = DimPlot(sce,reduction ="umap",label=T, group.by ="cell_annotion",cols=mycolors[6:15],label.size=2.5) CombinePlots(plots =list(p1, p2))
ggsave('plot/Cohort1_cell_annotion_plot.png', width =12, height =4)
### ---------------
###
### Create: Yuan.Sh
### Date: 2021-10-14 23:52:41
### Email:
### Blog: blog.csdn/qq_40966210
unparallel### Fujian Medical University
###hateyou
### ---------------
>课题项⽬合作以及咨询请联系：
After adviment, if you still have questions, you can nd me an E-mail asking for help
Best Regards,
Yuan.SH
---------------------------------------
plea contact me via the following ways:
(a) E-mail: yuansh3354@gmail/
(b) QQ: 1044532817
(c) WeChat: YuanSh181014
(d) Address: School of Basic Medical Sciences,
Fujian Medical University, Fuzhou,
Fujian 350108, China
---------------------------------------
