plot_tipping: Variation Line Plot
In microbiome/microbiome: Microbiome Analytics

plot_tipping

R Documentation

Variation Line Plot

Description

Plot variation in taxon abundance for many subjects.

Usage

plot_tipping(
  x,
  taxon,
  tipping.point = NULL,
  lims = NULL,
  shift = 0.001,
  xlim = NULL
)

Arguments

`x`	`phyloseq-class` object
`taxon`	Taxonomic group to visualize.
`tipping.point`	Optional. 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
`xlim`	Horizontal axis limits

Details

Assuming the sample_data(x) has 'subject' field and some subjects have multiple time points.

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')
p <- plot_tipping(pseq, 'Dialister', tipping.point=1)

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.