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 = NULL,
  uniqueId = "structID",
  nCores = 1
)

Arguments

spe

SpatialExperiment; An object of class SpatialExperiment containing spatial point data. Must contain colnames for correct assignment.

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 named list with structure assignments for each spatial point in spe. Points that do not overlap with any structure are assigned NA. Names correspond to colnames of the SpatialExperiment input object.

Examples

library("SpatialExperiment")
#> Loading required package: SingleCellExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     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
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     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’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#> 
#>     rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     anyMissing, rowMedians
data("sostaSPE")
allStructs <- reconstructShapeDensitySPE(sostaSPE,
    marks = "cellType", imageCol = "imageName",
    markSelect = "A", bndw = 3.5, thres = 0.045
)
# The function `assingCellsToStructures` needs colnames so we create them here
colnames(sostaSPE) <- paste0("cell_", c(1:dim(sostaSPE)[2]))

res <- assingCellsToStructures(
    spe = sostaSPE, allStructs = allStructs, imageCol = "imageName"
)
# Assign the structure assignment in the order of the columns in the `SpatialExperiment` object
colData(sostaSPE)$structAssign <- res[colnames(sostaSPE)]

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