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Plot an alluvial diagram of microbial relative abundance

Source: R/plot_alluvial.R
plot_alluvial.Rd

This function takes a MultiAssayExperiment object and returns a alluvial diagram of microbe relative abundances. The function takes a single covariate as an optional variable by which to create a grid of multiple plots. Note, the ggalluvial package is required to use this function.

Usage

plot_alluvial(
  dat,
  taxon_level,
  covariate_1 = NULL,
  covariate_time,
  palette_input = NULL,
  title = paste("Relative abundance at", taxon_level, "level"),
  subtitle = NULL
)

Arguments

dat

A MultiAssayExperiment object specially formatted as an animalcules output.

taxon_level

Character string indicating the level of taxonomy to aggregate the counts data. Must be the name of a column in MultiAssayExperiment::rowData(dat).

covariate_1

Character string giving the name of a column in MultiAssayExperiment::colData(dat) on which to create multiple plots. The default is NULL.

covariate_time

Character string giving the name of the discrete time-based covariate in the metadata to group abundances by.

palette_input

A character vector of colors that is at minimum the same length of the number of taxa (specified with taxon_level). The default is NULL and relies on ggplot2's default scheme.

title

A character string providing the plot title.

subtitle

A character string providing the plot subtitle. The default is NULL.

Value

A ggplot2 plot.

Details

If further manipulation of specific parameters is desired, users can add ggplot2 function calls to the output of the function.

Examples

in_dat <- system.file("extdata/MAE_small.RDS", package = "LegATo") |> readRDS()
plot_alluvial(in_dat, taxon_level = "family", covariate_1 = "Group", covariate_time = "Month",
              palette_input = rainbow(25))