plotAlphaDiv: Plot Alpha Diversity

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot Alpha Diversity

Description

Plot Alpha Diversity

Usage

plotAlphaDiv(
  dataset = NULL,
  method = "Chao1",
  factor = NULL,
  stratify = FALSE,
  facet.x = NULL,
  facet.y = NULL,
  flattenFactors = FALSE,
  param = FALSE,
  showStats = TRUE,
  width = 6,
  height = 4.5,
  add_xaxis = F,
  separateLegend = F
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
method	Method for alpha diversity calculation. One of either "chao1", "shannon", "simpson", "invsimpson", or "pd". Defaults to "chao1"
factor	Factor along which to compare alpha diversity between groups. Defaults to the active factor
stratify	Whether or not to stratify. Defaults to FALSE
facet.x	(Optional) A factor to stratify by horizontally
facet.y	(Optional) A factor to stratify by vertically
flattenFactors	Combine multiple factors
param	Whether to perform parametrized or nonparametrized univariate analysis of alpha diversity. Defaults to FALSE (nonparametrized)
showStats	Whether or not to show significance labels. Defaults to TRUE
width	Width of plot when saved, in inches. Increasing width and height will make text relatively smaller
height	Height of plot when saved, in inches. Increasing width and height will make text relatively smaller
add_xaxis	Whether to add x-axis labels. Defaults to FALSE
separateLegend	Whether to separate the legend from the plot. Defaults to FALSE

Value

Boxplot of alpha diversity of the groups

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