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

In spicyR: Spatial analysis of in situ cytometry data

Description

Get statistic from pairwise L curve of a single image.

Usage

getPairwise(
  cells,
  from = unique(cellType(cells)),
  to = unique(cellType(cells)),
  dist = NULL,
  window = "convex",
  window.length,
  Rs = NULL,
  sigma = NULL,
  minLambda = 0.05,
  fast = TRUE,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

cells	A SegmentedCells or data frame 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.
dist	The distance at which the statistic is obtained.
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.
fast	A logical describing whether to use a fast approximation of the inhomogeneous L-curves.
BPPARAM	A BiocParallelParam object.

Value

Statistic from pairwise L curve of a single image.

Examples

data("diabetesData")
pairAssoc <- getPairwise(diabetesData)

spicyR documentation built on March 17, 2021, 6:01 p.m.