plotAlpha: Plot alpha diversity

In microbiomeExplorer: Microbiome Exploration App

Description

This function plots the alpha diversity. See ?vegan::diversity for details on the available index

Usage

plotAlpha(
  aggdat,
  level,
  index = c("shannon", "simpson", "invsimpson", "richness"),
  x_var = "SAMPLE_ID",
  ylab = index,
  col_by = NULL,
  facet1 = NULL,
  facet2 = NULL,
  plotTitle = "",
  pwidth = 500,
  pheight = 150
)

Arguments

aggdat	aggregated MRExperiment
level	Feature level
index	Diversity index, one of "shannon", "simpson", "invsimpson" or "richness" (=number of features). Default is "shannon".
x_var	Phenotype to aggregate over on X-axis. Default by "SAMPLE_ID".
ylab	Y-axis label. Default is "Reads".
col_by	Phenotype for coloring.
facet1	Phenotype for facet 1.
facet2	Phenotype for facet 2.
plotTitle	Plot title. By default, no title is used.
pwidth	overall plot width; default is 650
pheight	overall plot height; default is 150

Value

plotly plot object

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
plotAlpha(aggdat, level = "genus", index = "shannon", x_var = "diet")

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.