Spatial smoother wrapper for SpatialExperiment and SingleCellExperiment objects

spatialSmoother(
  object,
  reducedDim2smooth = "PhiSpace",
  smoothReducedDim = TRUE,
  assay2smooth = "logcounts",
  smoothedReducedDim = NULL,
  smoothedAssay = NULL,
  x_coord = NULL,
  y_coord = NULL,
  k = 10,
  kernel = "linear",
  sigma = NULL,
  include_self = TRUE,
  verbose = TRUE
)

Arguments

object: SpatialExperiment or SingleCellExperiment object
reducedDim2smooth: Name of reduced dimension to smooth (default: "PhiSpace")
smoothReducedDim: Logical, whether to smooth reduced dimensions instead of gene expression
assay2smooth: Name of assay to smooth (for gene expression smoothing)
smoothedReducedDim: Name for the new smoothed reduced dimension (default: paste0(reducedDim2smooth, "_smoothed"))
smoothedAssay: Name for the new smoothed assay (default: paste0(assay2smooth, "_smoothed"))
x_coord: Column name in colData for x coordinates (required for SCE objects)
y_coord: Column name in colData for y coordinates (required for SCE objects)
k: Number of nearest neighbors (default: 10)
kernel: Kernel function: "gaussian", "uniform", or "linear" (default: "gaussian")
sigma: Bandwidth parameter for Gaussian kernel (default: auto-computed)
include_self: Whether to include the cell itself in smoothing (default: TRUE)
verbose: Whether to report progress with message() and show a progress bar (default: TRUE).

Value

Modified object with new smoothed assay or reduced dimension

Examples

set.seed(1)
ref <- logNormTransf(scuttle::mockSCE(ncells = 200, ngenes = 300))
query <- logNormTransf(scuttle::mockSCE(ncells = 100, ngenes = 300))
spe <- SpatialExperiment::SpatialExperiment(
  assays = list(logcounts = logcounts(query)),
  spatialCoords = cbind(x = runif(100), y = runif(100))
)
spe <- PhiSpace(ref, spe, phenotypes = "Cell_Cycle", refAssay = "logcounts",
                ncomp = 3)
spe <- spatialSmoother(spe, k = 5, verbose = FALSE)
reducedDimNames(spe)