amp_boxplot: Boxplot

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Boxplot

Description

Generates boxplots of the most abundant taxa.

Usage

amp_boxplot(
  data,
  group_by = NULL,
  sort_by = median,
  plot_type = "boxplot",
  point_size = 1,
  tax_aggregate = "Genus",
  tax_add = NULL,
  tax_show = 20,
  tax_empty = "best",
  tax_class = NULL,
  order_group = NULL,
  order_y = NULL,
  plot_flip = FALSE,
  plot_log = FALSE,
  adjust_zero = NULL,
  normalise = TRUE
)

Arguments

data	(required) Data list as loaded with amp_load.
group_by	Group the samples by a variable in the metadata.
sort_by	Generic function name to use for sorting most abundant taxa, fx mean, median, or sum. (default: median)
plot_type	Plot type. "boxplot" or "point". (default: "boxplot")
point_size	The size of points. (default: 1)
tax_aggregate	The taxonomic level to aggregate the OTUs. (default: "Genus")
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: 20)
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_class	Converts a specific phylum to class level instead, e.g. "p__Proteobacteria".
order_group	A vector to order the groups by.
order_y	A vector to order the y-axis by.
plot_flip	(logical) Flip the axes of the plot axis. (default: FALSE)
plot_log	(logical) Log10-scale the plot. (default: FALSE)
adjust_zero	Keep abundances of 0 in the calculation of medians by adding this value. (default: NULL)
normalise	(logical) Transform the OTU read counts to be in percent per sample. (default: TRUE)

Value

A ggplot2 object. If detailed_output = TRUE a list with a ggplot2 object and additional data.

Author(s)

Kasper Skytte Andersen [e-mail]

Mads Albertsen [e-mail]

See Also

amp_load

Examples

# Load example data
data("AalborgWWTPs")

# 10 boxplots grouped by WWTP with phylum name added
amp_boxplot(AalborgWWTPs,
  group_by = "Plant",
  tax_show = 10,
  tax_add = "Phylum"
)

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