amp_rankabundance: Rank abundance plot

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Rank abundance plot

Description

Generates a rank abundance curve (rank abundance vs cumulative read abundance), optionally with standard deviation from mean intervals.

Usage

amp_rankabundance(data, group_by, showSD = TRUE, log10_x = TRUE)

amp_rank_abundance(data, group_by, showSD = TRUE, log10_x = TRUE)

Arguments

data	(required) Data list as loaded with amp_load.
group_by	(required) Group the samples by a variable in the metadata.
showSD	Show standard deviation from mean or not. (default: TRUE)
log10_x	Log10-transform the x-axis or not. Often most variation is observed among the most abundant OTU's, log10-transforming the x-axis will highlight this better. (default: TRUE)

Details

Currently only OTU level is supported.

Value

A ggplot2 object.

Author(s)

Kasper Skytte Andersen [e-mail]

Mads Albertsen [e-mail]

See Also

amp_load

Examples

# Load example data
data("AalborgWWTPs")

# Rank abundance plot
amp_rankabundance(AalborgWWTPs, group_by = "Plant", showSD = TRUE, log10_x = TRUE)

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