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Evaluation of pairwise cell relationships, conditional on a 3rd population.

Source: R/Konditional.R
Kontextual.Rd

Kontextual identifies the relationship between two cell types which are conditional on the spatial behaviour of a 3rd cell population, for a particular radius (r).

Usage

Kontextual(
  cells,
  r,
  parentDf = NULL,
  from = NULL,
  to = NULL,
  parent = NULL,
  image = NULL,
  inhom = FALSE,
  edgeCorrect = TRUE,
  window = "convex",
  window.length = NA,
  weightQuantile = 0.8,
  includeZeroCells = TRUE,
  includeOriginal = TRUE,
  spatialCoords = c("x", "y"),
  cellType = "cellType",
  imageID = "imageID",
  cores = 1
)

Arguments

cells

A SingleCellExperiment, SpatialExperiment or a list of data.frames containing columns specifying the imageID, cellType, and x and y spatial coordinates.

r

Radii to evaluated pairwise relationships between from and to cells.

parentDf

A data frame from parentCombinations

from

The first cell type to be evaluated in the pairwise relationship.

to

The second cell type to be evaluated in the pairwise relationship.

parent

The parent population of the from cell type (must include from cell type).

image

A vector of images to subset the results to. If NULL we default to all images.

inhom

A logical value indicating whether to account for inhomogeneity.

edgeCorrect

A logical value indicating whether to perform edge correction.

window

Type of window for data, either `square`, `convex` or `concave`, passed into makeWindow

window.length

A tuning parameter for controlling the level of concavity when estimating concave windows. Passed into makeWindow

weightQuantile

A decimal value indicating what quantile of parent density used to weight the `from` cells.

includeZeroCells

A logical value indicating whether to include cells with zero counts in the pairwise association calculation.

includeOriginal

A logical value to return the original L function values along with the kontextual values.

spatialCoords

The columns which contain the x and y spatial coordinates.

cellType

The column which contains the cell types.

imageID

The column which contains image identifiers.

cores

Number of cores for parallel processing.

Value

A kontextualResult object

Examples

# Load data
data("kerenSCE")


CD4_Kontextual <- Kontextual(
  cells = kerenSCE,
  r = 50,
  from = "Macrophages",
  to = "Keratin_Tumour",
  parent = c("Macrophages", "CD4_Cell"),
  image = "6"
)


head(CD4_Kontextual)
#>   imageID                        test  original kontextual  r weightQuantile
#> 1       6 Macrophages__Keratin_Tumour -26.12355   1.917272 50            0.8
#>   inhom  edge includeZeroCells window window.length
#> 1  TRUE FALSE             TRUE convex            NA