rasterizeCellType — rasterizeCellType • SEraster

Function to rasterize cell type labels in spatially-resolved omics data represented as SpatialExperiment class.

This function assumes that the input is provided as a SpatialExperiment object or a list of SpatialExperiment objects.

Usage

rasterizeCellType(
  input,
  col_name,
  resolution = 100,
  square = TRUE,
  fun = "sum",
  n_threads = 1,
  BPPARAM = NULL,
  verbose = FALSE
)

Arguments

input: SpatialExperiment or list: Input data represented as a SpatialExperiment or list of SpatialExperiment. Each SpatialExperiment is assumed to have a colData slot containing cell type labels for observations as a data frame column and a spatialCoords slot containing spatial x,y coordinates of observations as matrix array. Further, x,y coordinates are assumed to be stored in column 1 and 2 of spatialCoords.
col_name: character: Column name of the colData object containing cell type labels for observations. If the input is a list, col_name is assumed to be present in all elements (SpatialExperiment) of the input.
resolution: integer or double: Resolution refers to the side length of each pixel for square pixels and the distance between opposite edges of each pixel for hexagonal pixels. The unit of this parameter is assumed to be the same as the unit of spatial coordinates of the input data.
square: logical: If TRUE (default), rasterize into square pixels. If FALSE, rasterize into hexagonal pixels.
fun: character: If "mean", pixel value for each pixel would be the proportion of each cell type based on the one-hot-encoded cell type labels for all cells within the pixel. If "sum", pixel value for each pixel would be the number of cells of each cell type based on the one-hot-encoded cell type labels for all cells within the pixel.
n_threads: integer: Number of threads for parallelization. Default = 1. Inputting this argument when the BPPARAM argument is missing would set parallel exeuction back-end to be BiocParallel::MulticoreParam(workers = n_threads). We recommend setting this argument to be the number of cores available (parallel::detectCores(logical = FALSE)). If BPPARAM argument is not missing, the BPPARAM argument would override n_threads argument.
BPPARAM: BiocParallelParam: Optional additional argument for parallelization. This argument is provided for advanced users of BiocParallel for further flexibility for setting up parallel-execution back-end. Default is NULL. If provided, this is assumed to be an instance of BiocParallelParam.
verbose: logical: Whether to display verbose output or warning. Default is FALSE

Value

If the input was given as SpatialExperiment, the output is returned as a new SpatialExperiment object with assay slot containing the feature (cell types) x observations (pixels) matrix (dgCmatrix), spatialCoords

slot containing spatial x,y coordinates of pixel centroids, and colData slot containing meta data for pixels (number of cells that were aggregated in each pixel, cell IDs of cells that were aggregated in each pixel, pixel type based on the square argument, pixel resolution based on the resolution argument, pixel geometry as sfc_POLYGON). If the input was provided as list

of SpatialExperiment, the output is returned as a new list of SpatialExperiment containing information described above for corresponding SpatialExperiment. Further, names(input) is inherited in the output.

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
#> 
#> 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, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#>     tapply, union, 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("merfish_mousePOA")

# check assay names for this particular SpatialExperiment object (you can see 
# that cell-type labels are stored in the "celltype" column)
head(colData(merfish_mousePOA))
#> DataFrame with 6 rows and 4 columns
#>                                         bregma      celltype  neurontype
#>                                      <numeric>   <character> <character>
#> 6d6b1d59-6f3b-4a9d-b5a4-8c8b073ae025     -0.29   OD Mature 2            
#> 76200644-c14a-4cfa-8752-2a02e5f10d20     -0.29 OD Immature 1            
#> 6b08ca36-b395-415a-bb34-d7b67550c35d     -0.29    Inhibitory         I-7
#> b9cb9cfb-fff7-426e-8c36-18fe428ca156     -0.29    Excitatory        E-13
#> 982cc0fc-6d11-4dc4-9ffc-c8c0cee48e6d     -0.29   OD Mature 2            
#> ee13ce4c-adf8-4602-9a21-23fdf91d28e0     -0.29    Inhibitory         I-7
#>                                        sample_id
#>                                      <character>
#> 6d6b1d59-6f3b-4a9d-b5a4-8c8b073ae025    sample01
#> 76200644-c14a-4cfa-8752-2a02e5f10d20    sample01
#> 6b08ca36-b395-415a-bb34-d7b67550c35d    sample01
#> b9cb9cfb-fff7-426e-8c36-18fe428ca156    sample01
#> 982cc0fc-6d11-4dc4-9ffc-c8c0cee48e6d    sample01
#> ee13ce4c-adf8-4602-9a21-23fdf91d28e0    sample01

# rasterize a single SpatialExperiment object
# make sure to specify the col_name argument
out <- rasterizeCellType(merfish_mousePOA, col_name = "celltype", fun = "sum")

# rasterize a single SpatialExperiment object with user-defined resolution and hexagonal pixels
out <- rasterizeCellType(merfish_mousePOA, col_name = "celltype", resolution = 200, 
square = FALSE, fun = "sum")

# rasterize a list of SpatialExperiment objects (in this case, permutated datasets 
# with 3 different rotations)
spe_list <- permutateByRotation(merfish_mousePOA, n_perm = 3)
out_list <- rasterizeCellType(spe_list, col_name = "celltype", resolution = 100, 
square = TRUE, fun = "sum")