plotBetaDiv: Plot Beta Diversity

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot Beta Diversity

Description

Plot Beta Diversity

Usage

plotBetaDiv(
  dataset = NULL,
  method = "bray",
  weighted = F,
  factor = NULL,
  stratify = F,
  spokes = T,
  ellipse = T,
  ci = 0.95,
  showStats = T,
  labelSamples = F,
  separateLegend = F
)

Arguments

dataset	MicroVis dataset. Defaults to the 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
factor	Factor along which to group samples for analysis. Defaults to the active factor
stratify	Another factor to stratify groups
spokes	Draw spokes from group centroids to each sample? Defaults to TRUE
ellipse	Draw a confidence interval ellipse for each group? Defaults to TRUE
ci	Confidence interval level for ellipses (value between 0 and 1). Defaults to 0.95
showStats	Show statistical results in the plot. Defaults to TRUE
labelSamples	Label the samples. Defaults to FALSE
separateLegend	Separate the lenged from the figure. Defaults to FALSE

Value

Scatter plot of the dissimilarity indices of the samples of each group

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