Seurat添加分组

# Get cell identity classes 获取细胞标识
Idents(pbmc_small)
#> ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA AGTCAGACTGCACA 
#>              0              0              0              0              0 
#> TCTGATACACGTGT TGGTATCTAAACAG GCAGCTCTGTTTCT GATATAACACGCAT AATGTTGACAGTCA 
#>              0              0              0              0              0 
#> AGGTCATGAGTGTC AGAGATGATCTCGC GGGTAACTCTAGTG CATGAGACACGGGA TACGCCACTCCGAA 
#>              2              2              2              2              2 

# Set cell identity classes 设置细胞标识
# Can be used to set identities for specific cells to a new level
Idents(pbmc_small, cells = 1:4) <- 'a'
head(Idents(pbmc_small))
#> ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA AGTCAGACTGCACA 
#>              a              a              a              a              0 
#> TCTGATACACGTGT 
#>              0 
#> Levels: a 0 1 2

# Can also set idents from a value in object metadata
colnames(pbmc_small[[]])
#> [1] "orig.ident"      "nCount_RNA"      "nFeature_RNA"    "RNA_snn_res.0.8"
#> [5] "letter.idents"   "groups"          "RNA_snn_res.1"  
Idents(pbmc_small) <- 'RNA_snn_res.1'
levels(pbmc_small)
#> [1] "0" "1" "2"

# Rename cell identity classes 重命名细胞标识分类，把0命名为A，把2命名为C
# Can provide an arbitrary amount of idents to rename
levels(pbmc_small)
#> [1] "0" "1" "2"
pbmc_small <- RenameIdents(pbmc_small, '0' = 'A', '2' = 'C')
levels(pbmc_small)
#> [1] "A" "C" "1"

# Set cell identity classes using SetIdent 使用setident设置细胞标识
cells.use <- WhichCells(pbmc_small, idents = '1') #选取idents=1的细胞
pbmc_small <- SetIdent(pbmc_small, cells = cells.use, value = 'B')#将这类细胞的标识设置为B

head(pbmc_small[[]])
#>                   orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
#> ATGCCAGAACGACT SeuratProject         70           47               0
#> CATGGCCTGTGCAT SeuratProject         85           52               0
#> GAACCTGATGAACC SeuratProject         87           50               1
#> TGACTGGATTCTCA SeuratProject        127           56               0
#> AGTCAGACTGCACA SeuratProject        173           53               0
#> TCTGATACACGTGT SeuratProject         70           48               0
#>                letter.idents groups RNA_snn_res.1
#> ATGCCAGAACGACT             A     g2             0
#> CATGGCCTGTGCAT             A     g1             0
#> GAACCTGATGAACC             B     g2             0
#> TGACTGGATTCTCA             A     g2             0
#> AGTCAGACTGCACA             A     g2             0
#> TCTGATACACGTGT             A     g1             0

#seurat对象添加分组（空分组）
integrated$cau <- NA

#seruat对象以active idents添加分组
celltype <- c("0"="exiting neurons",
              "1"= "dividing",
              "2"= "interneuron",
              "3"= "astrocytes",
              "4"= "exiting neurons",
              "5"= "IPC",
              "6"= "oligodrocyte",
              "7"= "dividing",
              "8"= "interneuron",
              "9"= "oligodrocyte",
              "10"= "oligodrocyte",
              "11"= "Microglia",
              "12"= "vascular",
              "13"= "oligodrocyte")

integrated <- RenameIdents(integrated,celltype)
integrated$cell_type <- integrated@active.ident

#按orig_ident分组
Idents(integrated) <- "orig.ident"
b <- integrated@meta.data$orig.ident
PFC <- b[1:755]
feiL <- b[756:length(b)]
PFC <- substr(PFC,8,nchar(PFC)-1)#nchar()——获取字符串长度
feiL <- substr(feiL,6,nchar(feiL)-1)
b <- c(PFC,feiL)#合并两个字符串，直接用c()
integrated@meta.data$tissue <- b

如图metadata成功出现tissue分组