Spatially shift an object

Shift the spatial locations of an object

Usage

# S4 method for class 'giotto'
spatShift(
  x,
  dx = 0,
  dy = 0,
  spat_unit = ":all:",
  feat_type = ":all:",
  images = ":all:"
)

# S4 method for class 'SpatExtent'
spatShift(x, dx = 0, dy = 0)

# S4 method for class 'spatLocsObj'
spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)

# S4 method for class 'data.frame'
spatShift(
  x,
  dx = 0,
  dy = 0,
  dz = 0,
  copy_obj = TRUE,
  geom = c("sdimx", "sdimy", "sdimz"),
  ...
)

# S4 method for class 'spatialNetworkObj'
spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)

# S4 method for class 'giottoPolygon'
spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)

# S4 method for class 'giottoPoints'
spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)

# S4 method for class 'giottoLargeImage'
spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)

# S4 method for class 'giottoImage'
spatShift(x, dx = 0, dy = 0, ...)

# S4 method for class 'giottoAffineImage'
spatShift(x, dx = 0, dy = 0, ...)

# S4 method for class 'affine2d'
spatShift(x, dx = 0, dy = 0, ...)

Arguments

x

object

dx

numeric. The shift on the x axis

dy

numeric. The shift on the y axis

spat_unit

character vector. spatial units to affect

feat_type

character vector. feature types to affect

images

character vector. Images to affect.

dz

numeric. The shift on the z axis

copy_obj

Default = TRUE

...

additional params to pass to methods

geom

character. Named vector of colnames of x, y, (z) coordinate columns. Default is c("sdimx", "sdimy", "sdimz")

Value

object with shifted spatial locations

Details

With the giotto object, the ":all:" token can be passed to spat_unit, feat_type, and images arguments to affect all available items.

Methods (by class)

• spatShift(spatialNetworkObj): Shift the locations of a spatialNetworkObj

Examples

g <- GiottoData::loadSubObjectMini("spatLocsObj")

spatShift(g)
#> An object of class spatLocsObj : "raw"
#> spat_unit : "aggregate"
#> provenance: z0 z1 
#> dimensions: 462 3 
#> preview   :
#>       sdimx     sdimy                                 cell_ID
#>       <num>     <num>                                  <char>
#> 1: 6637.881 -5140.465 100210519278873141813371229408401071444
#> 2: 6471.978 -4883.541 101161259912191124732236989250178928032
#> 3: 6801.610 -4968.685 101488859781016188084173008420811094152
#> 
#> ranges:
#>         sdimx     sdimy
#> [1,] 6401.412 -5146.747
#> [2,] 6899.108 -4700.326
#>