The [[ operator pulls either subobjects
(eg. v3 or v5 assays,
dimensional reduction information,
or nearest-neighbor graphs) or cell-level
meta data from a Seurat object
# S3 method for Seurat
[[(x, i = missing_arg(), ..., drop = FALSE, na.rm = FALSE)
# S3 method for Seurat
head(x, n = 10L, ...)
# S3 method for Seurat
tail(x, n = 10L, ...)Varies based on the value of i:
If i is missing, a data frame with cell-level meta data
If i is a vector with cell-level meta data names, a data frame
(or vector of drop = TRUE) with cell-level meta data requested
If i is a one-length character with the
name of a subobject, the
subobject specified by i
head: The first n rows of cell-level metadata
tail: The last n rows of cell-level metadata
See here for adding meta data with [[<-,
here for adding subobjects with [[<-, and
here for removing subobjects and cell-level meta
data with [[<-
Seurat object, validity, and interaction methods
$.Seurat(),
Seurat-class,
Seurat-validity,
[[<-,Seurat,
[[<-,Seurat,NULL,
dim.Seurat(),
dimnames.Seurat(),
merge.Seurat(),
names.Seurat(),
subset.Seurat()
# Get the cell-level metadata data frame
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
# Pull specific metadata information
head(pbmc_small[[c("letter.idents", "groups")]])
#> letter.idents groups
#> ATGCCAGAACGACT A g2
#> CATGGCCTGTGCAT A g1
#> GAACCTGATGAACC B g2
#> TGACTGGATTCTCA A g2
#> AGTCAGACTGCACA A g2
#> TCTGATACACGTGT A g1
head(pbmc_small[["groups", drop = TRUE]])
#> ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA AGTCAGACTGCACA
#> "g2" "g1" "g2" "g2" "g2"
#> TCTGATACACGTGT
#> "g1"
# Get a sub-object (eg. an `Assay` or `DimReduc`)
pbmc_small[["RNA"]]
#> Assay data with 230 features for 80 cells
#> Top 10 variable features:
#> PPBP, IGLL5, VDAC3, CD1C, AKR1C3, PF4, MYL9, GNLY, TREML1, CA2
pbmc_small[["pca"]]
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 1
#> Positive: SDPR, PF4, PPBP, TUBB1, CA2, TREML1, MYL9, PGRMC1, RUFY1, PARVB
#> Negative: HLA-DPB1, HLA-DQA1, S100A9, S100A8, GNLY, RP11-290F20.3, CD1C, AKR1C3, IGLL5, VDAC3
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 2
#> Positive: HLA-DPB1, HLA-DQA1, S100A8, S100A9, CD1C, RP11-290F20.3, PARVB, IGLL5, MYL9, SDPR
#> Negative: GNLY, AKR1C3, VDAC3, PGRMC1, TUBB1, PF4, TREML1, RUFY1, CA2, PPBP
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 3
#> Positive: S100A9, S100A8, RP11-290F20.3, AKR1C3, PARVB, GNLY, PPBP, PGRMC1, MYL9, TUBB1
#> Negative: HLA-DQA1, CD1C, IGLL5, HLA-DPB1, RUFY1, PF4, VDAC3, SDPR, TREML1, CA2
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 4
#> Positive: IGLL5, RP11-290F20.3, VDAC3, PPBP, TUBB1, TREML1, PF4, CA2, PARVB, MYL9
#> Negative: CD1C, AKR1C3, S100A8, GNLY, HLA-DPB1, HLA-DQA1, S100A9, PGRMC1, RUFY1, SDPR
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 5
#> Positive: MYL9, PARVB, IGLL5, TREML1, AKR1C3, PGRMC1, HLA-DPB1, S100A9, TUBB1, PF4
#> Negative: VDAC3, RP11-290F20.3, RUFY1, CD1C, HLA-DQA1, CA2, S100A8, PPBP, GNLY, SDPR
# Get the first 10 rows of cell-level metadata
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
#> TGGTATCTAAACAG SeuratProject 64 36 0
#> GCAGCTCTGTTTCT SeuratProject 72 45 0
#> GATATAACACGCAT SeuratProject 52 36 0
#> AATGTTGACAGTCA SeuratProject 100 41 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
#> TGGTATCTAAACAG A g1 0
#> GCAGCTCTGTTTCT A g1 0
#> GATATAACACGCAT A g1 0
#> AATGTTGACAGTCA A g1 0
# Get the last 10 rows of cell-level metadata
tail(pbmc_small)
#> orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
#> ATTCAGCTCATTGG SeuratProject 212 38 0
#> GGCATATGGGGAGT SeuratProject 172 29 0
#> ATCATCTGACACCA SeuratProject 168 37 0
#> GTCATACTTCGCCT SeuratProject 210 33 0
#> TTACGTACGTTCAG SeuratProject 228 39 0
#> GAGTTGTGGTAGCT SeuratProject 527 47 0
#> GACGCTCTCTCTCG SeuratProject 202 30 0
#> AGTCTTACTTCGGA SeuratProject 157 29 0
#> GGAACACTTCAGAC SeuratProject 150 30 0
#> CTTGATTGATCTTC SeuratProject 233 76 1
#> letter.idents groups RNA_snn_res.1
#> ATTCAGCTCATTGG A g2 0
#> GGCATATGGGGAGT A g1 0
#> ATCATCTGACACCA A g2 0
#> GTCATACTTCGCCT A g2 0
#> TTACGTACGTTCAG A g1 0
#> GAGTTGTGGTAGCT A g1 0
#> GACGCTCTCTCTCG A g2 0
#> AGTCTTACTTCGGA A g1 0
#> GGAACACTTCAGAC A g2 0
#> CTTGATTGATCTTC B g1 1