ggbiplot_vegan: GGbiplot prototype function

In inbo/inboggvegan: GGplot functions

GGbiplot prototype function

Description

Wrapper function around all geoms to construct a ggplot for vegan objects (rda, cca, capscale)

Usage

ggbiplot_vegan(x, ...)

## S3 method for class 'rda'
ggbiplot_vegan(x, ...)

## S3 method for class 'cca'
ggbiplot_vegan(x, ...)

## S3 method for class 'capscale'
ggbiplot_vegan(x, ...)

## S3 method for class 'princomp'
ggbiplot_vegan(x, ...)

## S3 method for class 'prcomp'
ggbiplot_vegan(x, ...)

## Default S3 method:
ggbiplot_vegan(x, choices = 1:2, scaling = 2,
  site_data = NULL, site_merge_by = "row.names", species_data = NULL,
  species_merge_by = "row.names", site_geom = "point",
  site_mapping = aes(label = Row.names), centroid_geom = "blank",
  centroid_mapping = aes(group = 1), ellipse_geom = "blank",
  ellipse_mapping = NULL, species_geom = "arrow",
  species_mapping = aes(label = Row.names), cor_circle_geom = "blank",
  cor_circle_mapping = NULL, lc_geom = "blank",
  lc_mapping = aes(label = Row.names), bp_geom = "blank",
  bp_mapping = NULL, cn_geom = "blank", cn_mapping = aes(label =
  .level), species_abbrev = FALSE, species_adjust = 1.1,
  ellipse_level = 0.68, base_colors = c("black", "red", "blue"),
  base_shapes = c(16, 16, 16), base_sizes = c(2, 2, 2),
  legend_position = "right", ...)

Arguments

x	vegan object
...	other arguments for ggbiplot_vegan.default
choices	which 2 components schould be visualized
scaling	used scaling (1 = site, 2 = species (default)). If scaling = 2, than the angle of the species (variables) matches the correlation
site_data	descriptor data for the sites
site_merge_by	merge the site descriptor with the vegan object on .Rownumbers (cbind), .Rownames or any other column (merge this column with the site scores matrix rownames)
species_data	descriptor data for the species
species_merge_by	merge species data (see site_merge_by)
site_geom	which geom to represent the sites "blank", "point", "text"
site_mapping	ggplot mapping in the format aes() but x and y must not be given, so for example (aes(color = Kolom1, size = Kolom2, label = Kolom3)). This should always contain the label argument if the geom is "text"
centroid_geom	representation of the site centroids ("blank", "point", "text")
centroid_mapping	ggplot mapping for the centroids (see site_mapping)
ellipse_geom	representation of the site probability density ellipses ("blank", "line")
ellipse_mapping	ggplot mapping for the ellipses
species_geom	representation of the species (or biometric variables) ("blank", "text", "arrow", "point")
species_mapping	ggplot mapping for the species
cor_circle_geom	representation of the correlation circle ("blank", "line")
cor_circle_mapping	ggplot mapping for the correlation circle
lc_geom	representation of linear constraints (see site_geom)
lc_mapping	see site_mapping but for the linear constraints
bp_geom	representation of the continuous environmental variables ("blank", "arrow", "text", "point")
bp_mapping	mapping of the continuous environmental variables
cn_geom	representation of the discrete environmental variables
cn_mapping	mapping of the discrete environmental variables
species_abbrev	logical that controls if species names (or variables when not working with vegetation data) should be abbreviated
species_adjust	adjustment of the species labels so they do not collide with the arrows
ellipse_level	probability density on which the ellipses should be based. 0.68 or 0.95 are the most logical choices (1 or 2 sd from the centroids)
base_colors	vector of 3 elements with the base colors of sites, species and environmental variables
base_shapes	vector of 3 elements with the base shapes for sites, species and environmental variables
base_sizes	vector of 3 elements with the base sizes for sites, species and environmental variables
legend_position	position of the legend "top", "bottom", "left", "right", "none"

inbo/inboggvegan documentation built on July 31, 2023, 6:51 p.m.