Add Fitted Vectors to Ordination plots

Fits arrows to show the direction of fastest increase in continuous environmental variables in ordination space.The arrows are scaled relative to their correlation coefficient, and they can be added to an ordination plot with geom_ordi_arrow().

stat_vectorfit(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  edata = NULL,
  formula = NULL,
  arrowmul = NULL,
  ...
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

geom

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

na.rm

Remove missing values (Not Yet Implemented).

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

edata

Environmental data where the continuous variables are found.

formula

Formula to select variables from edata. If missing, all continuos variables of edata are used.

arrowmul

Multiplier to arrow length. If missing, the multiplier is selected automatically so that arrows fit the current graph.

...

Other arguments passed to the functions.

Examples

library("vegan")
set.seed(1)
data(mite, mite.env)
m <- metaMDS(mite, trace = FALSE, trymax = 100)

## add fitted vectors for continuous variables
ordiggplot(m) +
  geom_ordi_point("sites") +
  geom_ordi_arrow("sites", stat = "vectorfit", edata = mite.env)
#> Warning: The following aesthetics were dropped during statistical transformation:
#> SubsDens, WatrCont, Substrate, Shrub, Topo
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> Warning: The following aesthetics were dropped during statistical transformation:
#> SubsDens, WatrCont, Substrate, Shrub, Topo
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?


## can be faceted
ordiggplot(m) + geom_ordi_point("sites") +
  geom_ordi_arrow("sites", stat = "vectorfit", edata = mite.env) +
  facet_wrap(mite.env$Topo)
#> Warning: The following aesthetics were dropped during statistical transformation:
#> SubsDens, WatrCont, Substrate, Shrub
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> Warning: The following aesthetics were dropped during statistical transformation:
#> SubsDens, WatrCont, Substrate, Shrub
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> Warning: The following aesthetics were dropped during statistical transformation:
#> SubsDens, WatrCont, Substrate, Shrub
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> Warning: The following aesthetics were dropped during statistical transformation:
#> SubsDens, WatrCont, Substrate, Shrub
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?