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 = TRUE,
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 |
logical. Default |
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 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)