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Spatial relationships between geometries

Source: R/methods-relate.R
relate.Rd

relate() returns a logical matrix indicating the presence or absence of a specific spatial relationships between the geometries in x and y.

Usage

# S4 method for class 'giottoSpatial,giottoSpatial'
relate(
  x,
  y,
  relation,
  pairs = TRUE,
  na.rm = TRUE,
  output = c("data.table", "matrix"),
  use_names = TRUE,
  ...
)

# S4 method for class 'giotto,giottoSpatial'
relate(
  x,
  y,
  ...,
  what = c("polygon", "spatlocs", "points"),
  spat_unit = NULL,
  feat_type = NULL,
  spat_locs_name = NULL
)

Arguments

x

spatial object with records to test

y

spatial object records to test relations against

relation

character. One of "intersects", "touches", "crosses", "overlaps", "within", "contains", "covers", "coveredby", "disjoint". Or a "DE-9IM" string such as "FF*FF****". See wikipedia or geotools doc

pairs

logical. If TRUE a two-column matrix is returned with the indices of the cases where the requested relation is TRUE. This is especially helpful when dealing with many geometries as the returned value is generally much smaller

na.rm

logical. If TRUE and pairs=TRUE, geometries in x for which there is no related geometry in y are omitted

output

character. "data.table" or "matrix". "data.table" is only possible when pairs=TRUE

use_names

logical. If TRUE, pairs=TRUE, and output="data.table" the IDs of the geometries will be used.

...

additional args to pass

what

character. Which type of spatial data in the giotto object to relate. One of "polygon", "spatlocs", "points"

spat_unit

spatial unit

feat_type

feature type

spat_locs_name

name of spatlocs to use if what = "spatlocs"

Value

data.table if output="data.table". matrix if output="matrix"

Examples

g <- GiottoData::loadGiottoMini("viz")
#> 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"
activeSpatUnit(g) <- "aggregate"
sl <- g[["spatial_locs"]][[1]]
gpoints <- g[["feat_info"]][[1]]
gpoly <- g[["spatial_info"]][[1]]

res1 <- relate(gpoints, gpoly, relation = "intersects")
res2 <- relate(gpoints, gpoly, relation = "intersects", use_names = FALSE)

selection <- system.file("extdata/viz_interactive_select.csv",
    package = "GiottoClass"
)
select_polys <- createGiottoPolygon(data.table::fread(selection))
#>   Selecting col "name" as poly_ID column
#>   Selecting cols "x" and "y" as x and y respectively
res <- relate(g, select_polys, relation = "intersects")
g[,res[y == "polygon1", x]]
#> An object of class giotto 
#> >Active spat_unit:  aggregate 
#> >Active feat_type:  rna 
#> dimensions    : 337, 25 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : z0 z1 aggregate 
#> features      : rna 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [z0][rna] raw
#>   [z1][rna] raw
#>   [aggregate][rna] raw normalized scaled pearson
#> spatial locations ----------------
#>   [z0] raw
#>   [z1] raw
#>   [aggregate] raw
#> spatial networks -----------------
#>   [aggregate] Delaunay_network kNN_network
#> spatial enrichments --------------
#>   [aggregate][rna] cluster_metagene
#> dim reduction --------------------
#>   [aggregate][rna] pca umap tsne
#> nearest neighbor networks --------
#>   [aggregate][rna] sNN.pca
#> attached images ------------------
#> images      : 4 items...
#> 
#> 
#> Use objHistory() to see steps and params used
g[,res[y == "polygon2", x]]
#> An object of class giotto 
#> >Active spat_unit:  aggregate 
#> >Active feat_type:  rna 
#> dimensions    : 337, 90 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : z0 z1 aggregate 
#> features      : rna 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [z0][rna] raw
#>   [z1][rna] raw
#>   [aggregate][rna] raw normalized scaled pearson
#> spatial locations ----------------
#>   [z0] raw
#>   [z1] raw
#>   [aggregate] raw
#> spatial networks -----------------
#>   [aggregate] Delaunay_network kNN_network
#> spatial enrichments --------------
#>   [aggregate][rna] cluster_metagene
#> dim reduction --------------------
#>   [aggregate][rna] pca umap tsne
#> nearest neighbor networks --------
#>   [aggregate][rna] sNN.pca
#> attached images ------------------
#> images      : 4 items...
#> 
#> 
#> Use objHistory() to see steps and params used
g[,res[y == "polygon3", x]]
#> An object of class giotto 
#> >Active spat_unit:  aggregate 
#> >Active feat_type:  rna 
#> dimensions    : 337, 245 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : z0 z1 aggregate 
#> features      : rna 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [z0][rna] raw
#>   [z1][rna] raw
#>   [aggregate][rna] raw normalized scaled pearson
#> spatial locations ----------------
#>   [z0] raw
#>   [z1] raw
#>   [aggregate] raw
#> spatial networks -----------------
#>   [aggregate] Delaunay_network kNN_network
#> spatial enrichments --------------
#>   [aggregate][rna] cluster_metagene
#> dim reduction --------------------
#>   [aggregate][rna] pca umap tsne
#> nearest neighbor networks --------
#>   [aggregate][rna] sNN.pca
#> attached images ------------------
#> images      : 4 items...
#> 
#> 
#> Use objHistory() to see steps and params used