plotBeta {microbiomeExplorer} | R Documentation

## Plot beta diversity

### Description

This functions plots the beta diversity as a PCoA plot.

### Usage

    plotBeta(
      aggdat,
      dim = c(1, 2),
      log = TRUE,
      dist_method = "bray",
      pcas = NULL,
      nfeatures = nrow(aggdat),
      col_by = NULL,
      shape_by = NULL,
      plotTitle = "",
      xlab = NULL,
      ylab = NULL,
      pt_size = 8,
      plotText = NULL,
      confInterval = NULL,
      allowWebGL = TRUE,
      pwidth = 550,
      pheight = 550
    )

### Arguments

`aggdat` | aggregated MRExperiment
`dim` | Vector of length 2 specifying which dimensions to plot.
`log` | Log2 transform data. Default is TRUE.
`dist_method` | Which distance method to use. See ?vegan::vegdist for more `vegdist()` for options. Default is "bray".
`pcas` | precalculated pcas to avoid recalculation via CalcPCs
`nfeatures` | Number of top features in terms of standard deviation. Default is all.
`col_by` | Phenotype for coloring.
`shape_by` | Phenotype for shape.
`plotTitle` | Plot title. By default, becomes PCoA (codedist.method).
`xlab` | X-axis label. By default, shows dimension and percent variance explained.
`ylab` | Y-axis label. By default, shows dimension and percent variance explained.
`pt_size` | the size of the markers
`plotText` | adonis text to be added to plot
`confInterval` | numeric value indicating confidence level for ellipses
`allowWebGL` | boolean indicating if WebGL should be used
`pwidth` | overall plot width; default is 550 (125 are added for legend)
`pheight` | overall plot height; default is 550

### Value

plotly plot object

### Examples

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

[Package microbiomeExplorer version 1.4.0 Index]