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)phyloseq-class.
The data about which you want to
plot and annotate the ordination.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."samples". The
currently supported options are
c("samples", "sites", "species", "taxa", "biplot", "split", "scree").
The option
``taxa'' is equivalent to ``species'' in this case, and similarly,
``samples'' is equivalent to ``sites''.
The options
"sites" and "species" result in a single-plot of just the
sites/samples or species/taxa of the ordination, respectively.
The "biplot" and "split" options result in a combined
plot with both taxa and samples, either combined into one plot (``biplot'')
or
separated in two facet panels (``split''), respectively.
The "scree" option results in a call to plot_scree,
which produces an ordered bar plot of the normalized eigenvalues
associated with each ordination axis.character-class or integer-class,
naming the index name or index of the desired axis for the horizontal
and vertical axes, respectively, in that order. The default value,
c(1, 2), specifies the first two axes of the provided ordination.NULL. Character string.
The name of the variable to map to
colors in the plot.
This can be a sample variable
(among the set returned by sample_variables(physeq) )
or
taxonomic rank
(among the set returned by rank_names(physeq)). Note that the color scheme is chosen automatically
by link{ggplot},
but it can be modified afterward with an additional layer using
scale_color_manual.
NULL. Character string.
The name of the variable to map
to different shapes on the plot.
Similar to color option, but for the shape if points. The shape scale is chosen automatically by link{ggplot},
but it can be modified afterward with an additional layer using
scale_shape_manual.
NULL. Character string.
The name of the variable to map to text labels on the plot.
Similar to color option, but for plotting text.NULL. Character string.
The main title for the graphic.FALSE. Logical.
Instead of returning a ggplot2-object, do you just want the relevant
data.frame that was used to build the plot? This is a
user-accessible option for obtaining the data.frame, in
in principal to make a custom plot that isn't possible with the
available options in this function. For contributing new functions
(developers), the
phyloseq-package provides/uses an internal function
to build the key features of the data.frame prior to plot-build.ggplot plot object, graphically summarizing
the ordination result for the specified axes.Also see the general wrapping function:
# 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")Run the code above in your browser using DataLab