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Subset part of an object with [

Source: R/methods-extract.R
subset_bracket.Rd

Extract values from Giotto classes. Providing empty brackets such as: x[] will usually extract the main contained data representation.

Usage

# S4 method for class 'gdtData,gIndex,gIndex,missing'
x[i, j]

# S4 method for class 'gdtData,logical,missing,missing'
x[i, j]

# S4 method for class 'gdtData,character,missing,missing'
x[i, j]

# S4 method for class 'gdtData,missing,numeric,missing'
x[i, j]

# S4 method for class 'gdtData,missing,logical,missing'
x[i, j]

# S4 method for class 'coordDataDT,ANY,ANY,missing'
x[i, j]

# S4 method for class 'coordDataDT,missing,ANY,missing'
x[i, j]

# S4 method for class 'coordDataDT,missing,character,missing'
x[i, j]

# S4 method for class 'coordDataDT,ANY,missing,missing'
x[i, j]

# S4 method for class 'coordDataDT,missing,missing,missing'
x[i, j]

# S4 method for class 'giottoPoints,gIndex,missing,missing'
x[i, j]

# S4 method for class 'metaData,missing,ANY,missing'
x[i, j]

# S4 method for class 'metaData,missing,character,missing'
x[i, j]

# S4 method for class 'metaData,ANY,missing,missing'
x[i, j]

# S4 method for class 'metaData,missing,missing,missing'
x[i, j]

# S4 method for class 'dimObj,ANY,ANY,missing'
x[i, j]

# S4 method for class 'dimObj,missing,missing,missing'
x[i, j]

# S4 method for class 'exprData,missing,ANY,missing'
x[i, j]

# S4 method for class 'exprData,ANY,missing,missing'
x[i, j]

# S4 method for class 'exprData,ANY,ANY,missing'
x[i, j]

# S4 method for class 'exprData,missing,missing,missing'
x[i, j]

# S4 method for class 'spatNetData,missing,missing,missing'
x[i, j]

# S4 method for class 'nnData,missing,missing,missing'
x[i, j]

# S4 method for class 'enrData,missing,missing,missing'
x[i, j]

# S4 method for class 'enrData,ANY,missing,missing'
x[i, j]

# S4 method for class 'enrData,missing,ANY,missing'
x[i, j]

# S4 method for class 'enrData,missing,character,missing'
x[i, j]

# S4 method for class 'spatGridData,missing,missing,missing'
x[i, j]

# S4 method for class 'giottoPoints,missing,missing,missing'
x[i, j]

# S4 method for class 'giottoPoints,gIndex,missing,missing'
x[i, j]

# S4 method for class 'giottoPoints,character,missing,missing'
x[i, j]

# S4 method for class 'giottoPoints,missing,gIndex,missing'
x[i, j]

# S4 method for class 'giottoPolygon,missing,missing,missing'
x[i, j]

# S4 method for class 'giottoPolygon,gIndex,missing,missing'
x[i, j]

# S4 method for class 'giottoPolygon,character,missing,missing'
x[i, j]

# S4 method for class 'giottoPolygon,missing,gIndex,missing'
x[i, j]

# S4 method for class 'terraVectData,gIndex,gIndex,missing'
x[i, j]

# S4 method for class 'affine2d,missing,missing,missing'
x[i, j]

Arguments

x

Giotto S4 object to subset information from

i, j

indices specifying elements to extract. Indices are numeric or character vectors, or empty

Value

Same as x unless brackets are empty in which case, the main internal representation is returned.

`[` methods

Return coordinates slot data.table from giotto S4

Select rows (i) and cols (j) from giotto S4 metaDT slot

Return metaDT slot data.table from giotto S4

Return coordinates slot matrix from giotto S4 dimObj

Select rows (i) and cols (j) from giotto S4 exprMat slot

Return exprMat slot Matrix object from giotto S4

Return spatNetData slot network data.table object from giotto S4

Return nnData slot igraph object from giotto S4

Return enrData slot enrichment data.table object from giotto S4

Return spatGridData slot data.table object from giotto S4

Return giottoPoints spatVector slot

Return giottoPolygon spatVector slot

See also

replace_bracket subset_dollar replace_dollar

Examples

gpoints <- GiottoData::loadSubObjectMini("giottoPoints")

# extract contained `SpatVector`
gpoints[]
#>  class       : SpatVector 
#>  geometry    : points 
#>  dimensions  : 79761, 3  (geometries, attributes)
#>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax)
#>  coord. ref. :  
#>  names       : feat_ID global_z feat_ID_uniq
#>  type        :   <chr>    <int>        <int>
#>  values      :    Mlc1        0            1
#>                 Gprc5b        0            2
#>                   Gfap        0            3

# subset by feature
gpoints[c("Mlc1", "Gfap")]
#> An object of class giottoPoints
#> feat_type : "rna"
#> Feature Information:
#>  class       : SpatVector 
#>  geometry    : points 
#>  dimensions  : 5464, 3  (geometries, attributes)
#>  extent      : 6400.037, 6899.441, -5149.827, -4700.029  (xmin, xmax, ymin, ymax)
#>  coord. ref. :  
#>  names       : feat_ID global_z feat_ID_uniq
#>  type        :   <chr>    <int>        <int>
#>  values      :    Mlc1        0            1
#>                   Gfap        0            3
#>                   Gfap        0            4
#> 

# subset by feature and colname
gpoints["Mlc1", c("feat_ID", "feat_ID_uniq")]
#> An object of class giottoPoints
#> feat_type : "rna"
#> Feature Information:
#>  class       : SpatVector 
#>  geometry    : points 
#>  dimensions  : 488, 2  (geometries, attributes)
#>  extent      : 6400.037, 6899.308, -5149.827, -4703.377  (xmin, xmax, ymin, ymax)
#>  coord. ref. :  
#>  names       : feat_ID feat_ID_uniq
#>  type        :   <chr>        <int>
#>  values      :    Mlc1            1
#>                   Mlc1           55
#>                   Mlc1          127
#> 

# subset by index
gpoints[seq(20)]
#> An object of class giottoPoints
#> feat_type : "rna"
#> Feature Information:
#>  class       : SpatVector 
#>  geometry    : points 
#>  dimensions  : 20, 3  (geometries, attributes)
#>  extent      : 6400.037, 6400.745, -5096.167, -4770.126  (xmin, xmax, ymin, ymax)
#>  coord. ref. :  
#>  names       : feat_ID global_z feat_ID_uniq
#>  type        :   <chr>    <int>        <int>
#>  values      :    Mlc1        0            1
#>                 Gprc5b        0            2
#>                   Gfap        0            3
#>