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 1.37.0
Index]