Get a SpatExtent — ext • GiottoClass

Get a SpatExtent of an object. This is the spatial minmax x and y that the object is mapped to.

Usage

# S4 method for class 'spatLocsObj'
ext(x, ...)

# S4 method for class 'giottoPolygon'
ext(x, ...)

# S4 method for class 'giottoPoints'
ext(x, ...)

# S4 method for class 'spatialNetworkObj'
ext(x, ...)

# S4 method for class 'giottoLargeImage'
ext(x, ...)

# S4 method for class 'giottoImage'
ext(x, ...)

# S4 method for class 'giotto'
ext(
  x,
  spat_unit = ":all:",
  feat_type = ":all:",
  all_data = TRUE,
  prefer = c("polygon", "spatlocs", "points", "images"),
  name = list(spatlocs = ":all:"),
  verbose = NULL,
  ...
)

# S4 method for class 'giottoAffineImage'
ext(x, ...)

# S4 method for class 'giottoPoints,SpatExtent'
ext(x) <- value

# S4 method for class 'giottoPolygon,SpatExtent'
ext(x) <- value

# S4 method for class 'giottoLargeImage,SpatExtent'
ext(x) <- value

# S4 method for class 'ANY,ANY'
ext(x) <- value

# S4 method for class 'giottoImage,SpatExtent'
ext(x) <- value

Arguments

x: spatial object
...: additional params to pass
spat_unit: character. Spatial unit to limit search to. If not provided, a default will be set.
feat_type: character. Feature type to limit search to for "points" information. If not provided, a default will be set.
all_data: logical. When TRUE (default), all spatial information designated by prefer will be searched and a combined SpatExtent will be returned. When FALSE, only the SpatExtent of the first existing data as ordered by prefer will be returned.
prefer: character vector. Order of preferred data to get extent from. allowed terms are "polygon", "spatlocs", "points", "images". This is also the default ordering. Omitting terms removes them from the search.
name: named list. Specific object names to check. List names should correspond to allowed terms in prefer. More than one name is allowed for only "images" at the moment, which produces a combined SpatExtent
verbose: be verbose
value: value to set. Accepts any object that ext() will work on

Value

SpatExtent

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"
# giotto %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ext(g) # defaults to checking first giottoPolygon extent
#> SpatExtent : 6391.46568586489, 6903.57332779812, -5153.89721175534, -4694.86823300896 (xmin, xmax, ymin, ymax)
ext(g, prefer = "spatlocs") # check first spatLocsObj extent
#> SpatExtent : 6401.14818002375, 6899.3228463116, -5147.19306531348, -4700.15708342436 (xmin, xmax, ymin, ymax)
# first spatLocsObj from a different spat_unit
ext(g, spat_unit = "aggregate", prefer = "spatlocs")
#> SpatExtent : 6401.41164725267, 6899.10802819571, -5146.74746408943, -4700.32590047134 (xmin, xmax, ymin, ymax)

# from first image object
ext(g, prefer = "image")
#> SpatExtent : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax)

# add a dummy image with different spatial extent
r <- terra::rast(array(seq(25), dim = c(5, 5)))
test <- createGiottoLargeImage(r)
ext(test) <- c(1e5, 1.1e5, 0, 10)
g <- setGiotto(g, test) # add image

# combined from all image objects
ext(g, prefer = "image", name = list(images = list_images_names(g)))
#> SpatExtent : 6400.029, 110000, -5150.007, 10 (xmin, xmax, ymin, ymax)

# combined from all spatial data types in giotto object
ext(g, all_data = TRUE, name = list(images = list_images_names(g)))
#> SpatExtent : 6391.46568586489, 110000, -5153.89721175534, 10 (xmin, xmax, ymin, ymax)

# spatLocsObj %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
sl <- getSpatialLocations(g)
ext(sl)
#> SpatExtent : 6402.43781589887, 6899.20308651186, -5146.72565198022, -4700.15708342436 (xmin, xmax, ymin, ymax)

# giottoPolygon %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# get extent
gpoly <- getPolygonInfo(g, return_giottoPolygon = TRUE)
ext(gpoly)
#> SpatExtent : 6399.24384990901, 6903.24298517207, -5152.38959073896, -4694.86823300896 (xmin, xmax, ymin, ymax)

# set extent
plot(gpoly) # before

ext(gpoly) <- ext(0, 20, 30, 60)
plot(gpoly) # after


# giottoPoints %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# get extent
gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE)
ext(gpoints)
#> SpatExtent : 6400.037, 6900.0317, -5149.9834, -4699.9785 (xmin, xmax, ymin, ymax)

# set extent
plot(gpoints) # before

ext(gpoints) <- ext(0, 2000, 3000, 6000)
plot(gpoints) # after