getKFunction {funkycells}

Get K function

Description

This function computes the K function between the two agents for each unit, potentially averaging over replicates, or repeated measures.

Usage

getKFunction(
  data,
  agents,
  unit,
  replicate = NULL,
  rCheckVals = NULL,
  xRange = NULL,
  yRange = NULL,
  edgeCorrection = "isotropic"
)

Arguments

data

Dataframe with column titles for at least x, y, agents, and unit. For consistency (and avoiding errors), use that order. Additionally, replicate can be added.

agents

Two value vector indicating the two agents to use for the K function, the first to the second. These should be in the unit column.

unit

String of the column name in data indicating a unit or base thing. Note this unit may have replicates.

replicate

(Optional) String of the column name in data indicating the unique replicates, or repeated measures.

rCheckVals

(Optional) Numeric vector indicating the radius to check. Note, if note specified, this could take a lot of memory, particularly with many units and replicates.

xRange, yRange

(Optional) Two value numeric vector indicating the min and max x / y values. Note this is re-used for all images. The default just takes the min and max from each image. This allows different sized images, but the edges are defined by some agent location.

edgeCorrection

(Optional) String indicating type of edgeCorrection(s) to apply when computing the K functions. Options include: "border", "bord.modif", "isotropic", "Ripley", "translate", "translation", "periodic", "none", "best" or "all" selects all options.

Value

data.frame with the first column being the checked radius and the remaining columns relating to the K function for each unit at those points. If a K function could not be computed, perhaps due to lack of data, an NA is returned for the K function.

Examples

KFunction <- getKFunction(
  agents = c("B", "Tumor"), unit = "Person",
  data = TNBC_pheno[TNBC_pheno$Person == 1, -1],
  rCheckVals = seq(0, 50, 1),
  edgeCorrection = "isotropic"
)