Identify cells matching certain criteria

Returns a list of cells that match a particular set of criteria such as identity class, high/low values for particular PCs, etc.

WhichCells(object, ...)

# S3 method for Assay
WhichCells(object, cells = NULL, expression, invert = FALSE, ...)

# S3 method for Seurat
WhichCells(
  object,
  cells = NULL,
  idents = NULL,
  expression,
  slot = "data",
  invert = FALSE,
  downsample = Inf,
  seed = 1,
  ...
)

Arguments

object

An object

...

Arguments passed on to CellsByIdentities

return.null

If no cells are requested, return a NULL; by default, throws an error

cells

Subset of cell names

expression

A predicate expression for feature/variable expression, can evaluate anything that can be pulled by FetchData; please note, you may need to wrap feature names in backticks (``) if dashes between numbers are present in the feature name

invert

Invert the selection of cells

idents

A vector of identity classes to keep

slot

Slot to pull feature data for

downsample

Maximum number of cells per identity class, default is Inf; downsampling will happen after all other operations, including inverting the cell selection

seed

Random seed for downsampling. If NULL, does not set a seed

Value

A vector of cell names

See also

FetchData

Examples

WhichCells(pbmc_small, idents = 2)
#>  [1] "AGGTCATGAGTGTC" "AGAGATGATCTCGC" "GGGTAACTCTAGTG" "CATGAGACACGGGA"
#>  [5] "TACGCCACTCCGAA" "CTAAACCTGTGCAT" "GTAAGCACTCATTC" "TTGGTACTGAATCC"
#>  [9] "CATCATACGGAGCA" "TACATCACGCTAAC" "GATAGAGAAGGGTG" "GCTCCATGAGAAGT"
#> [13] "CTGCCAACAGGAGC" "TTGCATTGAGCTAC" "CCTATAACGAGACG" "TTGAGGACTACGCA"
#> [17] "CATATAGACTAAGC" "GACATTCTCCACCT" "GCGTAAACACGGTT"
WhichCells(pbmc_small, expression = MS4A1 > 3)
#>  [1] "AGGTCATGAGTGTC" "AGAGATGATCTCGC" "GGGTAACTCTAGTG" "CATGAGACACGGGA"
#>  [5] "TACGCCACTCCGAA" "CTAAACCTGTGCAT" "GTAAGCACTCATTC" "TTGGTACTGAATCC"
#>  [9] "CATCATACGGAGCA" "TACATCACGCTAAC" "ATTACCTGCCTTAT" "GATAGAGATCACGA"
levels(pbmc_small)
#> [1] "0" "1" "2"
WhichCells(pbmc_small, idents = c(1, 2), invert = TRUE)
#>  [1] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA"
#>  [5] "AGTCAGACTGCACA" "TCTGATACACGTGT" "TGGTATCTAAACAG" "GCAGCTCTGTTTCT"
#>  [9] "GATATAACACGCAT" "AATGTTGACAGTCA" "CTAAACCTCTGACA" "CTAACGGAACCGAT"
#> [13] "AGATATACCCGTAA" "TACTCTGAATCGAC" "GCGCATCTTGCTCC" "GTTGACGATATCGG"
#> [17] "ACAGGTACTGGTGT" "GGCATATGCTTATC" "CATTACACCAACTG" "TAGGGACTGAACTC"
#> [21] "TACAATGATGCTAG" "CTTCATGACCGAAT" "AAGCAAGAGCTTAG" "CGGCACGAACTCAG"
#> [25] "GGTGGAGATTACTC" "GGCCGATGTACTCT" "CATGCGCTAGTCAC" "ATTCAGCTCATTGG"
#> [29] "GGCATATGGGGAGT" "ATCATCTGACACCA" "GTCATACTTCGCCT" "TTACGTACGTTCAG"
#> [33] "GAGTTGTGGTAGCT" "GACGCTCTCTCTCG" "AGTCTTACTTCGGA" "GGAACACTTCAGAC"