data.frame with a
subset of points according to a threshold and method. The
meaning of the threshold depends upon the method. See
argument description below. There are many useful
examples of phyloseq ordination graphics in the
phyloseq
online tutorials.
subset_ord_plot(p, threshold=0.05, method="farthest")ggplot object
created by plot_ordination. It contains the
complete data that you want to subset.0.05. This value determines a coordinate threshold
or population threshold, depending on the value of the
method argument, ultimately determining which
points are included in returned data.frame.c("farthest", "radial", "square"). Default is
"farthest". This determines how threshold will be
interpreted.
threshold. If threshold is greater than or
equal to 1, then all but threshold number
of points farthest from the origin are removed.
Otherwise, if threshold is less than 1, all
but threshold fraction of points farthests from
origin are retained.
threshold radial distance from the origin. Has the
effect of removing a circle of points from the plot,
centered at the origin.
threshold. Has the effect
of removing a ``square'' of points from the plot,
centered at the origin.
data.frame suitable for creating a
ggplot plot object, graphically summarizing
the ordination result according to previously-specified
parameters.
## See the online tutorials.
## http://joey711.github.io/phyloseq/subset_ord_plot-examples
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