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phyloseq (version 1.16.2)

subset_ord_plot: Subset points from an ordination-derived ggplot

Description

Easily retrieve a plot-derived 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 http://joey711.github.io/phyloseq/subset_ord_plot-examples{phyloseq online tutorials}.

Usage

subset_ord_plot(p, threshold=0.05, method="farthest")

Arguments

p
(Required). A ggplot object created by plot_ordination. It contains the complete data that you want to subset.
threshold
(Optional). A numeric scalar. Default is 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.
method
(Optional). A character string. One of c("farthest", "radial", "square"). Default is "farthest". This determines how threshold will be interpreted.

[object Object],[object Object],[object Object]

Value

  • A data.frame suitable for creating a ggplot plot object, graphically summarizing the ordination result according to previously-specified parameters.

See Also

http://joey711.github.io/phyloseq/subset_ord_plot-examples{phyloseq online tutorial} for this function.

plot_ordination

Examples

Run this code
## See the online tutorials.
## http://joey711.github.io/phyloseq/subset_ord_plot-examples

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