Find Spatially Variable Metabolites — FindSpatiallyVariableMetabolites • SpaMTP

Finds metabolites that display strong spatial patterns using MoransI. Each m/z value is ranked by MoransI score and the results are stored in the SpaMTP Seurat Object feature metadata.

Usage

FindSpatiallyVariableMetabolites(
  object,
  assay = "SPM",
  slot = "counts",
  image = "slice1",
  nfeatures = 2000,
  max_spots = 5000,
  seed = 1,
  verbose = TRUE
)

Arguments

object: SpaMTP Seurat class object contating the intensity values for each m/z
assay: Character string indicating which Seurat object assay to pull data form (default = "SPM").
slot: Character string indicating the assay slot to use to pull expression values form (default = "counts").
image: Character string defining the image to extract the tissue coordinates from (defualt = "slice1").
nfeatures: Numeric values defining the top number of features to mark as the top spatially variable (default = 2000).
max_spots: Maximum number of spots used to construct Seurat's dense Moran's I distance matrix. When the object is larger, spots are sampled deterministically using seed. Set to NULL to use every spot (default = 5000).
seed: Integer random seed used only when max_spots triggers subsampling (default = 1).
verbose: Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Value

Returns SpaMTP object containing the MoransI pvalue and rank stored in the assay feature meta.data

Examples

utils::str(formals(FindSpatiallyVariableMetabolites))
#> Dotted pair list of 8
#>  $ object   : symbol 
#>  $ assay    : chr "SPM"
#>  $ slot     : chr "counts"
#>  $ image    : chr "slice1"
#>  $ nfeatures: num 2000
#>  $ max_spots: num 5000
#>  $ seed     : num 1
#>  $ verbose  : logi TRUE
# SpaMTP.obj <- FindSpatiallyVariableMetabolites(SpaMTP)