demo/dune_plot_dcCA2.R

In douconca: Double Constrained Correspondence Analysis for Trait-Environment Analysis in Ecology

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)

CWM_SNC_env_trait_scores <- getPlotdata(out)
myplot <- plot(out)
# Huge uncertainty band for BF as
# management is in Condition() and there are one three BF plots,
# Without these separate lines use:
# plot(out,envfactor = NA)

names(myplot)
plot(out, gradient_description = c("corre", "tval"), 
     envfactor = NA, verbose = FALSE )

newnames_without_covariates <- 
  list(traits = c("SLA", "Height", "LDMC", "Seedmass", "annual", "perennial"),
       env = c("A1 horizon", "Moisture", "Type of use", "Manure"))

# modifying the plot
# Assign the plots to symbols and use grid.arrange to produce the plot you like, for example:
gg <- plot(out, gradient_description = c("corre", "weights"), 
           verbose = FALSE, newnames = newnames_without_covariates)

names(gg)

pl <- gg$separateplots
names(pl)

layout<- rbind(c(1, 2, 4), c(1, 3, 4))
gg_object <- gridExtra::grid.arrange(
  pl$CWM_SNC + ggplot2::xlab("env. and trait gradient"),
  pl$traits + ggplot2::ggtitle("cor"),
  pl$env+  ggplot2::ggtitle("w"),
  pl$species + ggplot2::ylab("trait complex"),
  layout_matrix = layout, widths = c(3, 1, 2),
  top = "", left = "", right = "")