amp_otu_network: Network plot

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Network plot

Description

Generates network plot of taxa and samples based on ggnet2.

Usage

amp_otu_network(
  data,
  min_abundance = 0,
  color_by = NULL,
  tax_aggregate = "Phylum",
  tax_add = NULL,
  tax_show = 10,
  tax_class = NULL,
  tax_empty = "best",
  normalise = TRUE,
  ...
)

Arguments

data	(required) Data list as loaded with amp_load.
min_abundance	Minimum taxa abundance pr. sample. (default: 0)
color_by	A metadata variable to color the samples by.
tax_aggregate	The taxonomic level to aggregate the OTUs. (default: "Phylum")
tax_add	Additional taxonomic level(s) to display, e.g. "Phylum". (default: "none")
tax_show	The number of taxa to show, or a vector of taxa names. (default: 10)
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.
normalise	(logical) Transform the OTU read counts to be in percent per sample. (default: TRUE)
...	Additional arguments passed on to ggnet2.

Details

See ggnet2

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]

See Also

amp_load

Examples

# Load example data
data("AalborgWWTPs")

# OTU network plot
amp_otu_network(AalborgWWTPs)

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