plotAlpha {microbiomeExplorer} | R Documentation

## Plot alpha diversity

### 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")

[Package microbiomeExplorer version 1.4.0 Index]