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Plot the CWMs and SNCs of a single dc-CA axis.

Source: R/plot_dcCA_CWM_SNC.R
plot_dcCA_CWM_SNC.Rd

plot_dcCA_CWM_SNC plots the CWMs and SNCs of a dc-CA axis against this axis, with optional centroids and colors for groups of sites and/or species if available in the data.

Usage

plot_dcCA_CWM_SNC(
  x,
  axis = 1,
  envfactor = NULL,
  traitfactor = NULL,
  facet = TRUE,
  newnames = NULL,
  remove_centroids = FALSE,
  with_lines = 2,
  formula = y ~ x,
  getPlotdata2plotdCCA = NULL
)

Arguments

x

results from dc_CA of class dcca.

axis

the axis number to get (default 1).

envfactor

name of row factor to display as color and lines in the CWM plot (default NULL). The default extracts the factor from the environmental model. If set to NA, no additional coloring and lines are displayed in plot.dcca. The parameter sets the groups variable in the CWM_SNC data frame of the return value/in the plot.

traitfactor

name of column factor to display as color and lines in the SNC plot (default NULL). The default extracts the factor from the trait model. If set to NA, no additional coloring and lines are displayed in plot.dcca. The parameter sets the groups variable in the CWM_SNC data frame of the return value/in the plot.

facet

logical. Default TRUE for CWMs and SNCs plots in separate panels. This parameter changes the position of the centroid names (from left to right for the environmental centroids). If facet = TRUE and with_lines = TRUE, the line fits ignore groups of species and of sites.

newnames

a list with two elements: names for traits and for environmental variables, default NULL for names derived from the result of scores.dcca with tidy = TRUE.

remove_centroids

logical to remove any centroids from the plot data (default FALSE). Can be a two-vector, e.g. c(TRUE, FALSE) to remove only the trait centroids.

with_lines

integer values (0,1,2). Default 2 for straight lines through groups of points, with confidence intervals around the lines. with_lines=1 drops the confidence intervals and with_lines=0 suppresses the lines.

formula

formula to use by ggplot geom_smooth (default y~x).

getPlotdata2plotdCCA

the results of an getPlotdata. Default NULL.

Value

a ggplot object

Details

The argument getPlotdata2plotdCCA is to allow some modifications of the data frame resulting from getPlotdata. The variable names and score levels should remain untouched. plot_dcCA_CWM_SNC uses the variables: dcCAk with axis number k and "CWM-SNC", "groups", "points", "sizeweight" for the y-axis, coloring, shape and size of items, respectively.

The current implementation does not distinguish groups of points, if there are two or more factors specified in the model. No lines are plotted if a single factor defines a model.

The function is used in plot.dcca.

Examples

data("dune_trait_env")

# rownames are carried forward in results
rownames(dune_trait_env$comm) <- dune_trait_env$comm$Sites

# must delete "Sites" from response matrix or data frame
Y <- dune_trait_env$comm[, -1] # must delete "Sites"

out <- dc_CA(formulaEnv = ~ A1 + Moist + Use + Manure + Condition(Mag),
             formulaTraits = ~ SLA + Height + LDMC + Seedmass + Lifespan,
             response = Y,
             dataEnv = dune_trait_env$envir,
             dataTraits = dune_trait_env$traits,
             verbose = FALSE)

plot_dcCA_CWM_SNC(out, facet = FALSE)