getPairwise: Get statistic from pairwise L curve of a single image.

In ellispatrick/spicyR: Spatial analysis of in situ cytometry data

Get statistic from pairwise L curve of a single image.

Description

Get statistic from pairwise L curve of a single image.

Usage

getPairwise(
  cells,
  imageID = "imageID",
  cellType = "cellType",
  spatialCoords = c("x", "y"),
  Rs = NULL,
  sigma = NULL,
  from = NULL,
  to = NULL,
  cores = 1,
  minLambda = 0.05,
  window = "convex",
  window.length = NULL,
  edgeCorrect = TRUE,
  includeZeroCells = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  imageIDCol = imageID,
  cellTypeCol = cellType,
  spatialCoordCols = spatialCoords,
  nCores = cores
)

Arguments

cells	A SummarizedExperiment that contains at least the variables x and y, giving the location coordinates of each cell, and cellType.
imageID	The name of the imageID column if using a SingleCellExperiment or SpatialExperiment.
cellType	The name of the cellType column if using a SingleCellExperiment or SpatialExperiment.
spatialCoords	The names of the spatialCoords column if using a SingleCellExperiment.
Rs	A vector of the radii that the measures of association should be calculated over.
sigma	A numeric variable used for scaling when fitting inhomogenous L-curves.
from	The 'from' cellType for generating the L curve.
to	The 'to' cellType for generating the L curve.
cores	Number of cores to use for parallel processing or a BiocParallel MulticoreParam or SerialParam object.
minLambda	Minimum value density for scaling when fitting inhomogeneous L-curves.
window	Should the window around the regions be 'square', 'convex' or 'concave'.
window.length	A tuning parameter for controlling the level of concavity when estimating concave windows.
edgeCorrect	A logical indicating whether to perform edge correction.
includeZeroCells	A logical indicating whether to include cells with zero counts in the pairwise association.
BPPARAM	{DEPRECATED} A BiocParallel MulticoreParam or SerialParam object.
imageIDCol	{DEPRECATED} The name of the imageID column if using a SingleCellExperiment or SpatialExperiment.
cellTypeCol	{DEPRECATED} The name of the cellType column if using a SingleCellExperiment or SpatialExperiment.
spatialCoordCols	{DEPRECATED} The names of the spatialCoords column if using a SingleCellExperiment.
nCores	{DEPRECATED} Number of cores to use for parallel processing or a BiocParallel MulticoreParam or SerialParam object. calculation.

Value

Statistic from pairwise L-curve of a single image.

Examples

data("diabetesData")
# Subset by imageID for fast example
selected_cells <- diabetesData[
  , SummarizedExperiment::colData(diabetesData)$imageID == "A09"
]
pairAssoc <- getPairwise(selected_cells)

ellispatrick/spicyR documentation built on Nov. 20, 2024, 6:39 a.m.