Processing the target spatial data

Usage

setup.srt(
  srt_data,
  srt_coords = NULL,
  th.spatial = 0.84,
  th.nonspatial = 0,
  th.gene.low = 0.01,
  th.gene.high = 0.99,
  remove_mt = TRUE,
  radius = "auto",
  verbose = FALSE
)

Arguments

srt_data: A gene x spot/cell matrix of gene expressions. Can be a matrix-like object or a Seurat/AnnData object
srt_coords: A matrix-like object with two columns (x and y coordinates of spots). If set to NULL and srt_data is Seurat/AnnData object, coords will be extracted from srt_data
th.spatial: A value between 0 and 1. Threshold on similarity of adjacent spots
th.nonspatial: A value between 0 and 1. Threshold on similarity of non-adjacent spots
th.gene.low: Minimum percentage of spots that a valid gene must be expressed in.
th.gene.high: Maximum percentage of spots that a valid gene must be expressed in.
remove_mt: Boolean. Whether mitochondrial genes must be removed.
radius: Adjacency radius. If set to 'auto' it is computed using the coordinates of spots
verbose: Boolean. Whether progress should be displayed.

Value

A list containing the processed srt data.

Examples

data(dot.sample)
dot.srt <- setup.srt(dot.sample$srt$counts, dot.sample$srt$coordinates)
#> Computing spatial radius