Get statistic from pairwise L curve of a single image.
Usage
getPairwise(
cells,
imageID = "imageID",
cellType = "cellType",
spatialCoords = c("x", "y"),
r = 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,
Rs = r
)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.
- r
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.
- Rs
{DEPRECATED} A vector of the radii that the measures of association should be calculated over. calculation.