plot_scree: General ordination eigenvalue plotter using ggplot2.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

General ordination eigenvalue plotter using ggplot2.

Description

Convenience wrapper for plotting ordination eigenvalues (if available) using a ggplot2-graphic.

Usage

plot_scree(ordination, title = NULL)

Arguments

ordination	(Required). An ordination object. Many different classes of ordination are defined by R packages. Ordination classes currently supported/created by the ordinate function are supported here. There is no default, as the expectation is that the ordination will be performed and saved prior to calling this plot function.
title	(Optional). Default NULL. Character string. The main title for the graphic.

Value

A ggplot plot object, graphically summarizing the ordination result for the specified axes.

See Also

plot_ordination

ordinate

distance

phyloseq online tutorials

Examples

# 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")

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.