plot_scree: General ordination eigenvalue plotter using ggplot2.
In phyloseq: Handling and analysis of high-throughput microbiome census data

Description Usage Arguments Value See Also Examples

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

1	plot_scree(ordination, title = NULL)

`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.

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

plot_ordination

ordinate

distance

phyloseq online tutorials

# 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")

Square root transformation
Wisconsin double standardization
Run 0 stress 0.153798 
Run 1 stress 0.1885161 
Run 2 stress 0.1577043 
Run 3 stress 0.1684335 
Run 4 stress 0.1930369 
Run 5 stress 0.1462585 
... New best solution
... Procrustes: rmse 0.04443251  max resid 0.1288562 
Run 6 stress 0.2767173 
Run 7 stress 0.1462102 
... New best solution
... Procrustes: rmse 0.08231987  max resid 0.1976477 
Run 8 stress 0.1459991 
... New best solution
... Procrustes: rmse 0.02192912  max resid 0.07824771 
Run 9 stress 0.2020778 
Run 10 stress 0.1875078 
Run 11 stress 0.1462585 
... Procrustes: rmse 0.08655941  max resid 0.229996 
Run 12 stress 0.1807685 
Run 13 stress 0.1537979 
Run 14 stress 0.153798 
Run 15 stress 0.149567 
Run 16 stress 0.1462585 
... Procrustes: rmse 0.08655395  max resid 0.2299845 
Run 17 stress 0.1615776 
Run 18 stress 0.1462585 
... Procrustes: rmse 0.08657888  max resid 0.2300238 
Run 19 stress 0.149042 
Run 20 stress 0.1462585 
... Procrustes: rmse 0.08655572  max resid 0.2299887 
*** No convergence -- monoMDS stopping criteria:
    18: stress ratio > sratmax
     2: scale factor of the gradient < sfgrmin
No eigenvalues found in ordination
NULL