Function to assign points / coordinates to structures

This function assigns each spatial coordinate in a SpatialExperiment object (spe) to the first intersecting structure from a given set of spatial structures.

Usage

assingCellsToStructures(
  spe,
  allStructs,
  imageCol,
  uniqueId = "structID",
  nCores = 1
)

Arguments

spe

SpatialExperiment; An object of class SpatialExperiment containing spatial point data.

allStructs

sf; A simple feature collection (sf object) representing spatial structures. Must contain a column which contains a unique identifier for each structure. Default = structID.

imageCol

character; The column name in spe and allStructs that identifies the corresponding image.

uniqueId

character; The column name in the simple feature collection for which to compute the assignment.

nCores

integer; The number of cores to use for parallel processing (default is 1).

Value

A vector with structure assignments for each spatial point in spe. Points that do not overlap with any structure are assigned NA.

Examples

library("SpatialExperiment")
#> Loading required package: SingleCellExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘MatrixGenerics’
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#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
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#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
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#> Attaching package: ‘BiocGenerics’
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#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
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#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
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#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
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#>     rowMedians
#> The following objects are masked from ‘package:matrixStats’:
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#>     anyMissing, rowMedians
data("sostaSPE")
allStructs <- reconstructShapeDensitySPE(sostaSPE,
    marks = "cellType", imageCol = "imageName",
    markSelect = "A", bndw = 3.5, thres = 0.045
)
colData(sostaSPE)$structAssign <- assingCellsToStructures(
    spe = sostaSPE, allStructs = allStructs, imageCol = "imageName"
)
if (require("ggplot2")) {
    cbind(
        colData(sostaSPE[, sostaSPE[["imageName"]] == "image1"]),
        spatialCoords(sostaSPE[, sostaSPE[["imageName"]] == "image1"])
    ) |>
        as.data.frame() |>
        ggplot(aes(x = x, y = y, color = structAssign)) +
        geom_point(size = 0.25) +
        coord_equal()
}
#> Loading required package: ggplot2