plotAbundance {microbiomeExplorer} | R Documentation

## Plot relative abundance

### Description

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

### Usage

    plotAbundance(
      aggdat,
      level,
      x_var = "SAMPLE_ID",
      ind = seq_len(10),
      plotTitle = "",
      ylab = "Reads",
      facet1 = NULL,
      facet2 = NULL,
      source = "A",
      pwidth = 650,
      pheight = 150
    )

### Arguments

`aggdat` | aggregated MRExperiment object
`level` | Feature level.
`x_var` | Phenotype to aggregate over on X-axis. Default by "SAMPLE_ID".
`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 650
`pheight` | overall plot height; default is 150

### Value

plotly plot

### Author(s)

Janina Reeder

### Examples

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

[Package microbiomeExplorer version 1.4.0 Index]