amp_frequency: Frequency plot

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Frequency plot

Description

Generates a barplot with frequency vs read abundance.

Usage

amp_frequency(
  data,
  group_by = "Sample",
  tax_class = NULL,
  tax_empty = "best",
  tax_aggregate = "OTU",
  weight = TRUE,
  normalise = TRUE,
  detailed_output = FALSE
)

Arguments

data	(required) Data list as loaded with amp_load.
group_by	Group the samples by a variable in the metadata. (default: "Sample")
tax_class	Converts a specific phylum to class level instead, e.g. "p__Proteobacteria".
tax_empty	How to show OTUs without taxonomic information. One of the following: "remove": Remove OTUs without taxonomic information. "best": (default) Use the best classification possible. "OTU": Display the OTU name.
tax_aggregate	The taxonomic level to aggregate the OTUs. (default: "OTU")
weight	(logical) Weight the frequency by abundance. (default: TRUE)
normalise	(logical) Transform 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. If detailed_output = TRUE a list with a ggplot2 object and additional data.

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, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H (2016): The activated sludge ecosystem contains a core community of abundant organisms, ISME Journal 10, 11-20. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ismej.2015.117")}

See Also

amp_load, amp_core, amp_venn

Examples

# Load example data
data("AalborgWWTPs")

# Frequency plot
amp_frequency(AalborgWWTPs)

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