Get statistic from pairwise L curve of a single image.
Usage
getPairwise(
cells,
from = NULL,
to = NULL,
window = "convex",
window.length = NULL,
Rs = c(20, 50, 100),
sigma = NULL,
minLambda = 0.05,
edgeCorrect = TRUE,
includeZeroCells = TRUE,
BPPARAM = BiocParallel::SerialParam(),
imageIDCol = "imageID",
cellTypeCol = "cellType",
spatialCoordCols = c("x", "y")
)Arguments
- cells
A SummarizedExperiment that contains at least the variables x and y, giving the location coordinates of each cell, and cellType.
- from
The 'from' cellType for generating the L curve.
- to
The 'to' cellType for generating the L curve.
- 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.
- Rs
A vector of the radii that the measures of association should be calculated.
- sigma
A numeric variable used for scaling when fitting inhomogeneous L-curves.
- minLambda
Minimum value for density for scaling when fitting inhomogeneous L-curves.
- edgeCorrect
A logical indicating whether to perform edge correction.
- includeZeroCells
A logical indicating whether to include cells with zero counts in the pairwise association calculation.
- BPPARAM
A BiocParallelParam object.
- imageIDCol
The name of the imageID column if using a SingleCellExperiment or SpatialExperiment.
- cellTypeCol
The name of the cellType column if using a SingleCellExperiment or SpatialExperiment.
- spatialCoordCols
The names of the spatialCoords column if using a SingleCellExperiment.