calculateDistanceMatrix-methods: Calculate distance matrix

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Calculate distance matrix

Description

Calculate distance matrix for the clusters in each tissue sample.

Usage

calculateDistanceMatrix(
  object,
  assay.type = "ST",
  sample.name = "Sample1",
  cluster.type = c("Cluster", "Subcluster"),
  spot_distance = 100,
  normalize = TRUE
)

## S4 method for signature 'CellRouter'
calculateDistanceMatrix(
  object,
  assay.type = "ST",
  sample.name = "Sample1",
  cluster.type = c("Cluster", "Subcluster"),
  spot_distance = 100,
  normalize = TRUE
)

Arguments

object	the CellRouter object.
assay.type	character; the type of data to use.
sample.name	character; the name of the tissue sample.
cluster.type	character; the column where the clusters are indicated. It could be either 'Cluster' or 'Subcluster'.
spot_distance	numeric; the distance between the center of the spots. The default is 100 micrometers. If this parameters is 1, the distance matrix will be relative to the rows and columns of the spots.
normalize	boolean; normalize the distances dividing by the total size of the tissue.

Value

the CellRouter object.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.