Plot a spaghetti volatility plot of microbial abundance for a given taxon

This function takes a MultiAssayExperiment object and returns a spaghetti plot of microbial abundance delineated by a unit, such as a subject.

Usage

plot_spaghetti(
  dat,
  covariate_time,
  covariate_1 = NULL,
  unit_var,
  taxon_level,
  which_taxon,
  palette_input = NULL,
  title = "Spaghetti Plot",
  subtitle = NULL
)

Arguments

dat: A MultiAssayExperiment object specially formatted as an animalcules output.
covariate_time: Character string giving the name of the discrete time-based covariate in the metadata to group abundances by.
covariate_1: Character string, the name of the covariate in `dat` by which to color and group samples. Default is NULL.
unit_var: Character string, the name of the column delineating the unit on which the microbial abundances are changing over time. This is likely something akin to a subject that repeated measurements are made on.
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).
which_taxon: Character string, the name of the taxon to plot at the specified taxon level.
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()
all_taxa <- get_top_taxa(in_dat, "phylum")
plot_spaghetti(in_dat, taxon_level = "phylum", covariate_1 = "Group", covariate_time = "Month",
              unit_var = "Subject", which_taxon = all_taxa$taxon[1],
              palette_input = rainbow(25))