plot_contributions: Plot species contributions for a single metabolite

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Plot species contributions for a single metabolite

Description

Plot species contributions for a single metabolite

Usage

plot_contributions(
  varShares,
  metabolite,
  metIDcol = "metID",
  include_zeros = F,
  include_residual = F,
  merge_threshold = 0.02,
  spec_threshold = 10,
  color_palette = NULL,
  order_spec = T,
  taxa_max = 15
)

Arguments

varShares	Dataset of contributions
metabolite	Compound to plot
include_zeros	Whether to plot taxa that do not have any contribution
include_residual	Whether to include the residual variation
merge_threshold	Threshold at which low-contributing species are merged into "other"
spec_threshold	Threshold number of minimum contributing species for merging into "other" to be applied
color_palette	Color palette to use for taxa in plot
order_spec	Whether to sort species by contribution size
taxa_max	If this compound has more than this many contributing taxa, only this number will be plotted

Value

plot of contributions

Examples

plot_contributions(varShares)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.