subset_ord_plot {phyloseq} | R Documentation

## 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 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. farthest Unlike the other two options, this option implies removing a certain fraction or number of points from the plot, depending on the value of `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. radial Keep only those points that are beyond `threshold` radial distance from the origin. Has the effect of removing a circle of points from the plot, centered at the origin. square Keep only those points with at least one coordinate greater than `threshold`. Has the effect of removing a “square” of points from the plot, centered at the origin.

### Value

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

### See Also

phyloseq online tutorial for this function.

`plot_ordination`

### Examples

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

[Package phyloseq version 1.24.2 Index]