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 'giottoLargeImage,missing,missing,missing'
x[i, j]
# S4 method for class 'giottoLargeImage,gIndex,missing'
x[[i, j, ...]]
# S4 method for class 'giottoImage,missing,missing,missing'
x[i, j]
# S4 method for class 'affine2d,missing,missing,missing'
x[i, j]
# S4 method for class 'processParam,missing,missing,missing'
x[i, j]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
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
#>