run.spatial.analysis: run.spatial.analysis

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis.

run.spatial.analysis

Description

run.spatial.analysis

Usage

run.spatial.analysis(
  dat,
  sample.col,
  pop.col,
  annot.cols = NULL,
  region.col = NULL,
  area.table = NULL,
  adj.dist = 20,
  x.col = "x",
  y.col = "y",
  distribution = TRUE,
  composition = TRUE,
  counts = TRUE,
  counts.per.area = TRUE,
  distance = TRUE,
  adjacency = TRUE,
  func = "mean"
)

Arguments

dat	NO DEFAULT. Data.table
sample.col	NO DEFAULT. Column that denotes 'samples'
pop.col	NO DEFAULT. Column that denotes 'samples'
annot.cols	DEFAULT = NULL. Annotation columns.
region.col	DEFAULT = NULL. Create a 'total' by default, and add specific ones if requested here
area.table	DEFAULT = NULL. Calculate 'total' automatically
adj.dist	DEFAULT = 20
x.col	DEFAULT = 'x'
y.col	DEFAULT = 'y'
distribution	DEFAULT = TRUE
composition	DEFAULT = TRUE
counts	DEFAULT = TRUE
counts.per.area	DEFAULT = TRUE
distance	DEFAULT = TRUE
adjacency	DEFAULT = TRUE
func	DEFAULT = 'mean'

ImmuneDynamics/Spectre documentation built on Nov. 12, 2023, 8:12 a.m.