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

Description Usage Arguments Value Examples

Description

Get statistic from pairwise L curve of a single image.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
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

1
2
data("diabetesData")
pairAssoc <- getPairwise(diabetesData)

ellispatrick/spicyR documentation built on March 22, 2021, 2:26 a.m.