General ordination eigenvalue plotter using ggplot2.
Convenience wrapper for plotting ordination eigenvalues (if available)
using a ggplot2-graphic.
plot_scree(ordination, title = NULL)
ordination |
(Required). An ordination object. Many different classes
of ordination are defined by |
title |
(Optional). Default |
A ggplot plot object, graphically summarizing
the ordination result for the specified axes.
# First load and trim a dataset
data("GlobalPatterns")
GP = prune_taxa(names(sort(taxa_sums(GlobalPatterns), TRUE)[1:50]), GlobalPatterns)
# Test plots (preforms ordination in-line, then makes scree plot)
plot_scree(ordinate(GP, "DPCoA", "bray"))
plot_scree(ordinate(GP, "PCoA", "bray"))
# Empty return with message
plot_scree(ordinate(GP, "NMDS", "bray"))
# Constrained ordinations
plot_scree(ordinate(GP, "CCA", formula=~SampleType))
plot_scree(ordinate(GP, "RDA", formula=~SampleType))
plot_scree(ordinate(GP, "CAP", formula=~SampleType))
# Deprecated example of constrained ordination (emits a warning)
#plot_scree(ordinate(GP ~ SampleType, "RDA"))
plot_scree(ordinate(GP, "DCA"))
plot_ordination(GP, ordinate(GP, "DCA"), type="scree")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.