plot_tipping {microbiome}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)

[Package microbiome version 1.4.2 Index]