plot_scree {phyloseq} | R Documentation

## 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")

[Package phyloseq version 1.28.0 Index]