View source: R/Ostats_multivariate_plot.R
Ostats_multivariate_plot  R Documentation 
This function plots the overlap of traits among species for each community in multivariate space, showing projections of trait hypervolumes into twodimensional space for all pairs of traits.
Ostats_multivariate_plot( plots, sp, traits, overlap_dat = NULL, use_plots = NULL, colorvalues = NULL, plot_points = TRUE, contour_level, axis_expansion = 0.01, contour_buffer_factor = 0.25, panel_height = 3, panel_width = 3, units = "cm", hypervolume_args = list() )
plots 
Site identity: a vector of names of each community. 
sp 
Taxon identity: a vector of species or taxa names. 
traits 
A matrix or data frame with rows representing individuals and columns representing traits. 
overlap_dat 
Optional: an object containing the output of

use_plots 
a vector of sites to plot. If NULL, the function will plot all the sites. 
colorvalues 
Vector of color values for the density polygons. Defaults to a viridis palette if none provided. 
plot_points 
whether to plot individual data points in addition to the hypervolume slices. Default is TRUE. 
contour_level 
level at which to plot contour lines. If not provided by the user, a message is issued stating the default plotting level is 0.01. 
axis_expansion 
multiplicative expansion factor by which to expand the x and y axes around the hypervolume contours before plotting. Default is 0.01. 
contour_buffer_factor 
multiplicative expansion factor by which to expand the x and y axes in all directions, relative to the range of the axis, before calculating the hypervolume contours for plotting. If this is not set to a sufficiently large value, the contour lines of the hypervolumes will be cut off. Default value is 0.25 (25% expansion of the axis limits in all directions). 
panel_height 
height of the individual plot panels, in units given by 
panel_width 
height of the individual plot panels, in units given by 
units 
units for panel height and width. Default is centimeters. 
hypervolume_args 
additional arguments to pass to 
Some of the code for generating contour lines is modified from
plot.HypervolumeList
.
Twodimensional projections of species trait hypervolumes for each pair of traits,
plotted together for each community to show how they overlap each other.
The overlap value obtained as output from Ostats_multivariate
is labelled on each community graph, if provided by the user.
The class of the returned object is Ostats_plot_object
. Calling
print
on this object will invoke a method to draw the plot using
grid.draw
.
If more than one community is provided, a list of objects of class
Ostats_plot_object
will be returned.
Ostats_multivariate
for generating multivariate Ostatistics
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.