mvdist: Distance Calculation

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Distance Calculation

Description

Distance Calculation

Usage

mvdist(
  dataset = NULL,
  method = "bray",
  weighted = F,
  allFactors = T,
  factors = NULL
)

Arguments

dataset	MicroVis dataset. Defaults to active dataset
method	Method for dissimilarity calculation. One of either "bray", "euclidean", "jaccard", "unifrac", "manhattan", "canberra", "clark", "kulczynski", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao", "mahalanobis", "chisq" or "chord"
weighted	(Optional) If method is set to "unifrac", whether to perform weighted or unweighted unifrac. Defaults to FALSE
allFactors	When performing distance calculation, only include samples in the active subgroups of all factors? Defaults to TRUE. Otherwise, user can specify which factors using the factor parameter (explained below)
factors	(Optional) Specify factors to filter samples by

Value

Dissimilarity matrix and other associated details of the calculation

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.