plotAvgAbundance: Plot average relative abundance

In microbiomeExplorer: Microbiome Exploration App

Description

This function plots the average relative abundance of the top abundant features.

Usage

plotAvgAbundance(
  aggdat,
  level,
  ind = seq_len(10),
  plotTitle = "",
  ylab = "Reads",
  facet1 = NULL,
  facet2 = NULL,
  source = "A",
  pwidth = 500,
  pheight = 150
)

Arguments

aggdat	aggregated MRExperiment object
level	Feature level.
ind	Indices of top abundant features to plot. Rest of features are aggregated and displayed as "other".
plotTitle	Plot title. Default shows no title.
ylab	Y-axis label. Default is "Reads"
facet1	Phenotype for facet 1.
facet2	Phenotype for facet 2.
source	name of the plot (needed for event handling); default is "A"
pwidth	overall plot width; default is 500
pheight	overall plot height; default is 150

Value

plotly plot

Author(s)

Janina Reeder

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
plotAvgAbundance(aggdat, level = "genus")

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