Compute Self-Distance Matrices for Multiple Cell Types

This function computes within-cell-type distance matrices for each cell type when multiple cell types are present. Unlike the standard computeDistance which only computes cross-type distances for multiple cell types, this function computes self-distances (within each cell type).

Usage

computeSelfDistance(
  object,
  distType = c("Euclidean2D", "Euclidean3D", "Morphology-Aware"),
  xDistScale = 1,
  yDistScale = 1,
  zDistScale = 1,
  normalizeDistance = TRUE,
  truncateLowDist = TRUE,
  verbose = TRUE,
  overwrite = FALSE
)

# S4 method for class 'CoProSingle'
computeSelfDistance(
  object,
  distType = c("Euclidean2D", "Euclidean3D", "Morphology-Aware"),
  xDistScale = 1,
  yDistScale = 1,
  zDistScale = 1,
  normalizeDistance = TRUE,
  truncateLowDist = TRUE,
  verbose = TRUE,
  overwrite = FALSE
)

# S4 method for class 'CoProMulti'
computeSelfDistance(
  object,
  distType = c("Euclidean2D", "Euclidean3D", "Morphology-Aware"),
  xDistScale = 1,
  yDistScale = 1,
  zDistScale = 1,
  normalizeDistance = TRUE,
  truncateLowDist = TRUE,
  verbose = TRUE,
  overwrite = FALSE
)

Arguments

object

A CoPro object with multiple cell types

distType

Type of distance to compute: "Euclidean2D", "Euclidean3D", or "Morphology-Aware"

xDistScale

Scale for x distance, default = 1

yDistScale

Scale for y distance, default = 1

zDistScale

Scale for z distance, default = 1

normalizeDistance

Whether to normalize distance? The normalization will make sure that the 0.01% cell-cell distance will become 0.01, thus ensuring consistent scaling across cell types. Default = TRUE

truncateLowDist

Whether to truncate small distances so that cells that are nearly overlapping do not have super small distances. Default = TRUE.

verbose

Whether to print info about the computation progress

overwrite

Whether to overwrite existing distance matrices. If FALSE, will add self-distance matrices to existing cross-type distances. Default = FALSE

Value

CoPro object with self-distance matrices added to the distances slot

Examples

if (FALSE) { # \dontrun{
# Assume you have a CoPro object with multiple cell types
# First compute cross-type distances
object <- computeDistance(object)

# Then add self-distances
object <- computeSelfDistance(object)

# Now you have both cross-type and self-type distance matrices
} # }