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Identify cells in small bits outside the main piece of tissue

Source: R/debris.R
findDebrisCells.Rd

This is used for quality control (QC), as the small bits are likely to be low quality technical artifacts and are not informative to spatial analyses. Please confirm the quality of those cells by checking the histology image with ImageJ or QuPath.

Usage

# S4 method for class 'matrix'
findDebrisCells(
  x,
  max_cells = 5,
  distance_cutoff = 50,
  BNPARAM = NULL,
  BPPARAM = SerialParam()
)

# S4 method for class 'sfc'
findDebrisCells(
  x,
  max_cells = 5,
  distance_cutoff = 50,
  BNPARAM = NULL,
  BPPARAM = SerialParam()
)

# S4 method for class 'sf'
findDebrisCells(
  x,
  max_cells = 5,
  distance_cutoff = 50,
  BNPARAM = NULL,
  BPPARAM = SerialParam()
)

# S4 method for class 'SpatialExperiment'
findDebrisCells(
  x,
  max_cells = 5,
  distance_cutoff = 50,
  BNPARAM = NULL,
  BPPARAM = SerialParam()
)

Arguments

x

Object with spatial coordinates of cells. Can be a SpatialExperiment or SpatialFeatureExperiment object, a matrix with 2 columns for x and y coordinates of cells, or a sf or sfc object with cell geometries.

max_cells

Maximum number of cells for a clump of cells to be considered debris.

distance_cutoff

Minimum distance of cell to the tissue for it to be considered debris, in the same unit as in x.

BNPARAM

A BiocNeighborParam object specifying the algorithm to find k nearest neighbors and distance based neighbors with nn_method = "bioc". For distance based neighbors, only KmknnParam and VptreeParam are applicable.

BPPARAM

A BiocParallelParam object for multithreading. Only used for k nearest neighbor and distance based neighbor with nn_method = "bioc".

Value

Depends on the method:

Spatial(Feature)Experiment

The same object with a logical column "is_debris" added to colData.

Matrix and sf(c)

A logical vector indicating whether each cell is debris.

Details

How this function works: A distance-based spatial neighborhood graph is computed, with distance_cutoff as the distance cutoff. Then disjoint connected subgraphs are found. Cells in subgraphs with max_cells or fewer cells are considered debris.