plot.dcca {douconca} | R Documentation |
Plot a single dc-CA axis with CWMs, SNCs, trait and environment scores.
Description
plot.dcca
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
## S3 method for class 'dcca'
plot(
x,
...,
axis = 1,
gradient_description = "correlation",
envfactor = NULL,
traitfactor = NULL,
nspecies = 20,
species_groups = NULL,
widths = c(5, 1, 1),
newnames = NULL,
facet = TRUE,
remove_centroids = FALSE,
with_lines = TRUE,
verbose = TRUE
)
Arguments
x |
results from |
... |
unused. |
axis |
the axis number to get (default 1). |
gradient_description |
character or 2-character vector for the trait
and environmental gradient, respectively specifying what to plot in the
vertical line plots to describe the dc-CA axis (trait and environmental
gradients). Default: |
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 |
nspecies |
integer. Default |
species_groups |
name of a variable in |
widths |
relative widths of the CWM-SNC plot, the correlation/weight
plot and the species plot. (see |
newnames |
a list with two elements: names for traits and for
environmental variables, default |
facet |
logical. Default |
remove_centroids |
logical to remove any centroids from the plot data
(default |
with_lines |
logical. Default |
verbose |
logical. Default |
Details
If you want to set new names, look at the names with all arguments default,
i.e. myplot <- plot(x)
, and then consult
myplot$nameList$newnames
for the order of the names of traits and
environmental variables. Note that covariates should not be in the list of
names. Contribution (in the definition of species selection in
nspecies
) is defined (as in CA) as the total species abundance in
the (possibly, closed) data multiplied by the square of the score on
the axis.
If the plot.dcca
returns the error "Error in grid.Call"
,
enlarge the plotting area or use verbose = FALSE
and assign the
result.
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 + Mag,
formulaTraits = ~ SLA + Height + LDMC + Seedmass + Lifespan,
response = Y,
dataEnv = dune_trait_env$envir,
dataTraits = dune_trait_env$traits,
verbose = FALSE)
dat <- getPlotdata(out)
names(dat)
names(dat$CWM_SNC)
levels(dat$CWM_SNC$groups)
plot(out)