Utility function: extracting data from a dc_CA object for plotting a single axis by your own code or plot.dcca.

getPlotdata extracts data from a dc_CA object for plotting the CWMs and SNCs of a single axis.

Usage

getPlotdata(
  x,
  axis = 1,
  envfactor = NULL,
  traitfactor = NULL,
  newnames = NULL,
  facet = TRUE,
  remove_centroids = FALSE
)

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.
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.
facet: logical. Default TRUE for CWMs and SNCs plots in separate panels. If FALSE, this parameter changes the position of the environmental centroid names (from left to right).
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.

Value

A list with three components

CWM_SNC: a data.frame containing plot data
trait_env_scores: a vector of scores per trait/environment
newNameList: a vector of new names to be used in the plot

Details

The current implementation sets the traitfactor to NA if the trait model contains more than a single trait factor and the envfactor to NA if the environmental model contains more than a single environmental factor.

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)
#> [1] "CWM_SNC"          "trait_env_scores" "oldNameList"      "newNameList"     
names(dat$CWM_SNC)
#>  [1] "dcCA1"         "score"         "label"         "CWM-SNC"      
#>  [5] "weight"        "type"          "points"        "sizeweight"   
#>  [9] "smoothweight"  "xforsmooth"    "groups"        "names"        
#> [13] "centroidnames"
levels(dat$CWM_SNC$groups)
#> [1] "SF"        "BF"        "HF"        "NM"        "annual"    "perennial"

plot(out)