dissimilarity_to_distance_importance_plot: Display species importance plot based on a weighted Euclidean...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Display species importance plot based on a weighted Euclidean distance transformation of dissimilarities.

Description

Display species importance plot based on a weighted Euclidean distance transformation of dissimilarities.

Usage

dissimilarity_to_distance_importance_plot(
  x,
  scaled_weights = TRUE,
  mark_removed = TRUE
)

Arguments

x	Result of dissimilarity_to_distance function
scaled_weights	Logical; if TRUE, scaled weights will be plotted
mark_removed	Logical; if TRUE, species that were removed from distance will be highlighted with a separate symbol on a plot

Details

Species importance measures the contribution of individual species to the overall dissimilarity between the samples.

Value

ggplot-object.

See Also

dissimilarity_to_distance

Examples

library(vegan); library(smacof)
data(varespec)

# Estimate weighted Euclidean distance
bc_to_eucl <- dissimilarity_to_distance(varespec, dist_type = "bray", drop_species = T, importance_percentile = 0.05, show_plot = F)

# Plot species weigths
dissimilarity_to_distance_importance_plot(bc_to_eucl)

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.