hotplot: Univariate Bimodality Plot

In microbiome: Microbiome Analytics

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 [e-mail]

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)

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.