amp_venn: Venn diagram of core OTUs

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Venn diagram of core OTUs

Description

Calculates the number of "core" OTUs shared by groups given thresholds for how frequent the OTUs should be above a certain abundance. Also returns the average abundance of the OTUs in a particular group.

Usage

amp_venn(
  data,
  group_by = NULL,
  cut_a = 0.1,
  cut_f = 80,
  text_size = 5,
  normalise = TRUE,
  detailed_output = FALSE
)

Arguments

data	(required) Data list as loaded with amp_load.
group_by	Group the data based on a sample metadata variable. amp_venn currently only supports a maximum of 3 different groups.
cut_a	Abundance cutoff in percent. OTU's below this abundance are excluded from the analysis. (default: 0.1)
cut_f	Frequency cutoff in percent. OTU's within the top cut_f of the reads are considered a "core" OTU. (default: 80)
text_size	Size of the plotted text. (default: 5)
normalise	(logical) Normalise the OTU read counts to be in percent per sample. (default: TRUE)
detailed_output	(logical) Return additional details or not. If TRUE, it is recommended to save to an object and then access the additional data by View(object$data). (default: FALSE)

Value

A ggplot2 object.

Preserving relative abundances in a subset of larger data

See ?amp_filter_samples or the ampvis2 FAQ.

Author(s)

Kasper Skytte Andersen [e-mail]

Mads Albertsen [e-mail]

References

[Saunders et al, 2016](https://www.nature.com/articles/ismej2015117)

See Also

amp_load

Examples

# Load example data
data("AalborgWWTPs")

# Venn diagram grouped by WWTP
amp_venn(AalborgWWTPs, group_by = "Plant")

MadsAlbertsen/ampvis2 documentation built on Jan. 28, 2024, 7:12 a.m.