hotplot {microbiome} | R Documentation

## Univariate Bimodality Plot

### Description

Coloured bimodality plot.

### Usage

    hotplot(
      x,
      taxon,
      tipping.point = NULL,
      lims = NULL,
      shift = 0.001,
      log10 = TRUE
    )

### Arguments

`x` | `phyloseq-class` object
`taxon` | Taxonomic group to visualize.
`tipping.point` | Indicate critical point for abundance variations to be highlighted.
`lims` | Optional. Figure X axis limits.
`shift` | Small constant to avoid problems with zeroes in log10
`log10` | Use log10 abundances for the OTU table and tipping point

### Value

`ggplot` object

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

See citation('microbiome')

### Examples

    data(atlas1006)
    pseq <- subset_samples(atlas1006, DNA_extraction_method == 'r')
    pseq <- transform(pseq, 'compositional')
    # Set a tipping point manually
    tipp <- .3/100 # .3 percent relative abundance
    # Bimodality is often best visible at log10 relative abundances
    p <- hotplot(pseq, 'Dialister', tipping.point=tipp, log10=TRUE)

[Package microbiome version 1.12.0 Index]