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Plot a fitted Neutral Model to Microbial Community Data

Source: R/plot_neutral_model.R
plot_neutral_model.Rd

This function plots ASV/OTUs log abundances into a fitted neutral model of microbial abundance-occupancy distribution. ASV/OTUs that are Core, As predicted (i.e. Neutral), Below and Above model predictions are drawn with distinct point colors, see details.

Usage

plot_neutral_model(fit_result)

Arguments

fit_result

A list-like object returned by fit_neutral_model().

Value

A ggplot2 object.

A ggplot object with:

  • x-axis: log10(mean abundance) (log10(otu_rel));

  • y-axis: Occupancy (otu_occ);

  • Points colored by membership/fit class as described above;

  • Neutral-model curve (solid) with 95\

  • An inset white label reporting R\(^2\) and m taken directly from fit_result$goodness_of_fit.

The function does not recompute statistics; it only visualizes the supplied predictions and metrics.

Details

Points are split into four groups for display:

  • Not core (as predicted) – background points;

  • Core (as predicted) – core taxa whose occupancy matches the model;

  • Core (above prediction) – core taxa above the 95\

  • Core (below prediction) – core taxa below the 95\

See also

fit_neutral_model

Examples

library(BRCore)
data("switchgrass_core", package = "BRCore")

switchgrass_core_fit <- fit_neutral_model(
  otu_table = switchgrass_core$otu_table,
  core_set = switchgrass_core$increase_core,
  abundance_occupancy = switchgrass_core$abundance_occupancy
)
#> Waiting for profiling to be done...
#> Warning: SNCM `stats::dnorm()` produced a warning during MLE: NaNs produced
#> Warning: Binomial model `stats::dnorm()` produced a warning during MLE: NaNs produced
#> Warning: Poisson model `stats::dnorm()` produced a warning during MLE: NaNs produced
#> ℹ Neutral model fitting:
#> • Average individuals per community (N): 1000
#> • Binomial model using rounded N: 1000
#> • Poisson model using N: 1000
#> • Maximum likelihood estimation using N: 1000, and starting parameters: mu = 0,
#>   sigma = 0.1
#> Warning: SNCM `stats::dnorm()` produced a warning during MLE: NaNs produced
#> Warning: Binomial model `stats::dnorm()` produced a warning during MLE: NaNs produced
#> Warning: Poisson model `stats::dnorm()` produced a warning during MLE: NaNs produced
#> ✔ Model fitting complete!

p <- plot_neutral_model(switchgrass_core_fit)
print(p)