plot_dcCA_CWM_SNC {douconca} | R Documentation |
Plot the CWMs and SNCs of a single dc-CA axis.
Description
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 |
axis |
the axis number to get (default 1). |
envfactor |
name of row factor to display as color and lines in the CWM
plot (default |
traitfactor |
name of column factor to display as color and lines in
the SNC plot (default |
facet |
logical. Default |
newnames |
a list with two elements: names for traits and for
environmental variables, default |
remove_centroids |
logical to remove any centroids from the plot data
(default |
with_lines |
integer values (0,1,2). Default |
formula |
formula to use by ggplot geom_smooth (default y~x). |
getPlotdata2plotdCCA |
the results of an |
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: dcCA
k 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
.
Value
a ggplot object
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)