Get or set the cell cluster labels from a celda SingleCellExperiment object or celda model object.

Return or set the cell cluster labels determined by celda_C or celda_CG models.

celdaClusters(x, altExpName = "featureSubset")

# S4 method for SingleCellExperiment
celdaClusters(x, altExpName = "featureSubset")

# S4 method for celdaModel
celdaClusters(x)

celdaClusters(x, altExpName = "featureSubset") <- value

# S4 method for SingleCellExperiment
celdaClusters(x, altExpName = "featureSubset") <- value

Arguments

x	Can be one of A SingleCellExperiment object returned by celda_C, or celda_CG, with the matrix located in the useAssay assay slot. The a altExp slot with name altExpName will be used. Rows represent features and columns represent cells. Celda model object.
altExpName	The name for the altExp slot to use. Default "featureSubset".
value	Character vector of cell cluster labels for replacements. Works only if x is a SingleCellExperiment object.

Value

One of

• Character vector if x is a SingleCellExperiment object. Contains cell cluster labels for each cell in x.

• List if x is a celda model object. Contains cell cluster labels (for celda_C and celdaCG Models) and/or feature module labels (for celda_G and celdaCG Models).

Examples

data(sceCeldaCG)
celdaClusters(sceCeldaCG)
#>   [1] 1 2 2 2 1 1 3 1 1 2 3 2 4 3 2 1 2 4 4 1 3 5 3 2 1 3 3 2 3 3 5 3 2 5 5 3 4
#>  [38] 4 3 2 1 2 1 1 2 3 4 2 5 3 5 1 1 3 1 3 3 1 4 5 4 4 1 3 5 2 5 2 1 3 1 2 4 1
#>  [75] 5 2 1 3 4 4 3 5 1 1 4 4 4 1 1 3 3 1 3 1 1 4 4 3 5 3 4 3 4 4 1 3 4 4 1 3 1
#> [112] 3 4 3 1 3 3 3 3 3 5 4 4 4 4 1 1 4 1 4 1 4 1 1 1 5 4 1 4 3 5 4 4 5 4 3 3 3
#> [149] 1 4 4 4 1 4 1 4 3 3 5 4 1 1 4 4 3 4 1 3 2 4 4 3 1 4 1 5 1 3 4 5 1 4 4 3 4
#> [186] 3 5 4 5 5 5 5 5 5 2 5 1 2 3 2 5 5 5 2 1 5 5 2 4 2 1 1 5 5 5 5 5 5 2 2 5 2
#> [223] 5 1 2 5 1 5 2 5 5 5 1 2 1 5 2 5 3 5 5 2 3 5 5 1 3 2 5 5 5 2 5 4 5 5 5 5 5
#> [260] 5 1 3 2 5 2 5 2 3 2 5 2 5 5 1 1 5 5 1 4 5 5 5 3 3 1 2 1 2 3 3 2 1 1 3 1 1
#> [297] 1 3 1 3 3 3 2 3 3 5 5 1 1 3 3 3 1 3 3 3 3 1 1 3 3 3 1 3 5 2 1 1 1 1 1 3 1
#> [334] 2 3 3 1 3 5 1 3 1 3 5 3 3 3 1 1 5 1 3 3 3 4 1 4 3 4 3 1 2 1 1 4 2 1 4 4 3
#> [371] 5 1 4 5 1 3 5 3 3 1 3 5 1 4 4 4 3 3 1 3 1 5 1 3 3 5 3 1 1 1 3 1 2 1 2 4 1
#> [408] 2 4 3 1 4 1 5 1 3 2 1 5 2 1 5 2 4 1
#> Levels: 1 2 3 4 5
data(celdaCGMod)
celdaClusters(celdaCGMod)
#> $z
#>   [1] 2 1 1 1 2 2 3 2 2 1 3 1 4 3 1 2 1 4 4 2 3 5 3 1 2 3 3 1 3 3 5 3 1 5 5 3 4
#>  [38] 4 3 1 2 1 2 2 1 3 4 1 5 3 5 2 2 3 2 3 3 2 4 5 4 4 2 3 5 1 5 1 2 3 2 1 4 2
#>  [75] 5 1 2 3 4 4 3 5 2 2 4 4 4 2 2 3 3 2 3 2 2 4 4 3 5 3 4 3 4 4 2 3 4 4 2 3 2
#> [112] 3 4 3 2 3 3 3 3 3 5 4 4 4 4 2 2 4 2 4 2 4 2 2 2 5 4 2 4 3 5 4 4 5 4 3 3 3
#> [149] 2 4 4 4 2 4 2 4 3 3 5 4 2 2 4 4 3 4 2 3 1 4 4 3 2 4 2 5 2 3 4 5 2 4 4 3 4
#> [186] 3 5 4 5 5 5 5 5 5 1 5 2 1 3 1 5 5 5 1 2 5 5 1 4 1 2 2 5 5 5 5 5 5 1 1 5 1
#> [223] 5 2 1 5 2 5 1 5 5 5 2 1 2 5 1 5 3 5 5 1 3 5 5 2 3 1 5 5 5 1 5 4 5 5 5 5 5
#> [260] 5 2 3 1 5 1 5 1 3 1 5 1 5 5 2 2 5 5 2 4 5 5 5 3 3 2 1 2 1 3 3 1 2 2 3 2 2
#> [297] 2 3 2 3 3 3 1 3 3 5 5 2 2 3 3 3 2 3 3 3 3 2 2 3 3 3 2 3 5 1 2 2 2 2 2 3 2
#> [334] 1 3 3 2 3 5 2 3 2 3 5 3 3 3 2 2 5 2 3 3 3 4 2 4 3 4 3 2 1 2 2 4 1 2 4 4 3
#> [371] 5 2 4 5 2 3 5 3 3 2 3 5 2 4 4 4 3 3 2 3 2 5 2 3 3 5 3 2 2 2 3 2 1 2 1 4 2
#> [408] 1 4 3 2 4 2 5 2 3 1 2 5 1 2 5 1 4 2
#> 
#> $y
#>   [1]  7  5  1  8  1  4 10  9  2  4  7 10 10  5  3 10  2 10  9  5  9  3  5  7  6
#>  [26]  9  9  4  8  2  9  5  4  5  9  5  5  4  4  6  5  8  8  5  1  6 10  9  7  1
#>  [51]  4  3  7  9  6 10  9 10  7  6  8  6  9  5  4  5  9  9 10  5  4  3  8  7  9
#>  [76]  6  2  3  7  6  3  4  9  3  9 10  4 10  7  1  1 10 10  1  6  1  6  9  5  4
#>