plot_ordination | R Documentation |
There are many useful examples of phyloseq ordination graphics in the
phyloseq online tutorials.
Convenience wrapper for plotting ordination results as a
ggplot2
-graphic, including
additional annotation in the form of shading, shape, and/or labels of
sample variables.
plot_ordination(physeq, ordination, type = "samples", axes = 1:2, color = NULL, shape = NULL, label = NULL, title = NULL, justDF = FALSE)
physeq |
(Required). |
ordination |
(Required). An ordination object. Many different classes
of ordination are defined by |
type |
(Optional). The plot type. Default is |
axes |
(Optional). A 2-element vector indicating the axes of the
ordination that should be used for plotting.
Can be |
color |
(Optional). Default Note that the color scheme is chosen automatically
by |
shape |
(Optional). Default The shape scale is chosen automatically by |
label |
(Optional). Default |
title |
(Optional). Default |
justDF |
(Optional). Default |
A ggplot
plot object, graphically summarizing
the ordination result for the specified axes.
Many more examples are included in the phyloseq online tutorials.
Also see the general wrapping function:
plot_phyloseq
# See other examples at # http://joey711.github.io/phyloseq/plot_ordination-examples data(GlobalPatterns) GP = prune_taxa(names(sort(taxa_sums(GlobalPatterns), TRUE)[1:50]), GlobalPatterns) gp_bray_pcoa = ordinate(GP, "CCA", "bray") plot_ordination(GP, gp_bray_pcoa, "samples", color="SampleType")
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