Construct Spatial Metacells from Single-Cell Spatial Data

This function computes spatial metacells from single-cell spatial transcriptomics. Spatial metacells represent aggregated expression profiles for spatially proximal cells. The function utilizes k-nearest neighbor (KNN) weighting to aggregate expression profiles from neighboring cells and generate metacell expression profiles for each cell type.

Usage

GetSpatialMetacells(
  normdata,
  metadata,
  X = "X",
  Y = "Y",
  CellType = "CellType",
  spotCoord = NULL,
  k = 20,
  radius = 50,
  min.cells.per.region = 1,
  ncores = 4
)

Arguments

normdata

A matrix or data frame representing normalized gene expression data, where rows correspond to genes and columns correspond to cells.

metadata

A data frame containing metadata associated with each cell. Must include spatial coordinates (e.g., X and Y) as well as cell type annotations. The row names of the metadata must match the column names of the normdata.

X

Character string specifying the column name in metadata containing the X spatial coordinates.

Y

Character string specifying the column name in metadata containing the Y spatial coordinates.

CellType

Character string specifying the column name in metadata containing the cell type annotations.

k

Integer specifying the number of nearest spatial neighbors for constructing metacells.

radius

Numeric value specifying the radius (in units of spatial coordinates) within which neighboring cells are considered.

min.cells.per.region

Integer specifying the minimum number of cells required in each spatial neighborhood to compute metacells.

ncores

Integer specifying the number of CPU cores to use for parallel processing (default: 4).

bin

Character string specifying the column name in metadata containing the spatial neighborhood identifier.

bin.X

Character string specifying the column name in metadata containing the X spatial coordinates of spatial neighborhoods.

bin.Y

Character string specifying the column name in metadata containing the Y spatial coordinates of spatial neighborhoods.

Value

A matrix containing the spatial metacell expression profiles, with rows representing individual genes and columns representing metacells.

Examples

library(data.table)
library(Seurat)
library(SpatialEcoTyper)
scdata <- fread("https://spatialecotyper.stanford.edu/inc/inc.public.vignettes.php?file=Melanoma1_subset_counts.tsv.gz",
                sep = "\t",header = TRUE, data.table = FALSE)
rownames(scdata) <- scdata[, 1]
scdata <- as.matrix(scdata[, -1])
normdata = NormalizeData(scdata)
scmeta <- read.table("https://spatialecotyper.stanford.edu/inc/inc.public.vignettes.php?file=Melanoma1_subset_scmeta.tsv",
                      sep = "\t",header = TRUE, row.names = 1)

# Construct spatial metacells from single-cell spatial data
metacells <- GetSpatialMetacells(normdata = normdata, metadata = scmeta,
                                 X = "X", Y = "Y", CellType = "CellType")
#> Error in spotCoord %>% group_by(SpotID) %>% summarize(X = median(X), Y = median(Y)) %>%     as.data.frame: could not find function "%>%"
head(metacells)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'metacells' not found