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Vertical ggplot2 line plot of ordination scores

Source: R/plot_species_scores_bk.R
plot_species_scores_bk.Rd

plot_species_scores_bk creates a vertical line plot of ordination scores with selection criterion for which scores to plot with names.

Usage

plot_species_scores_bk(
  species_scores,
  ylab = "scores",
  threshold = 7,
  y_lab_interval = 0.5,
  speciesname = NULL,
  scoresname = "RDA1",
  selectname = "Fratio1",
  speciesgroup = NULL,
  expand = 0.2,
  verbose = TRUE
)

Arguments

species_scores

a species-by-scores matrix, a data frame with row names (species names) or a tibble with variable with name speciesname containing species names and a column or variable with name scoresname containing the scores (default: "RDA1"), e.g. species scores from library vegan.

ylab

y-axis label. Default: $b_k$.

threshold

species with criterion (specified by selectname) higher than the threshold are displayed. Default: 7 (which is the threshold F-ratio for testing a single regression coefficient at p = 0.01 with 60 df for the error in a multiple regression of each single species onto the condition and the ordination axis). If selectname is not in species_scores, the threshold is divided by 14, so that the default is 0.5.

y_lab_interval

interval of the y-axis ticks. A tick at no effect (0) is always included; default: 0.5.

speciesname

name of the variable containing the species names (default NULL uses row names).

scoresname

name of the column or variable containing the species scores to be plotted (default "RDA1").

selectname

name of the column or variable containing the criterion for the selection of species to be displayed. Default: "Fratio1"; if selectname is not found in species_scores, set to scoresname.

speciesgroup

name of the factor, the levels of which receive different colors in the vertical plot.

expand

amount of extension of the line plot (default 0.2).

verbose

logical for printing the number of species with names out of the total number (default: TRUE).

Value

a ggplot object

Details

The absolute value of the criterion values is taken before selection, so that also the species scores of the ordination can serve as a criterion (e.g. selectname = "RDA1"). The function has been copied from the PRC package at https://github.com/CajoterBraak/PRC.

The function is used in plot.dcca.

Examples

data("dune_trait_env")

# rownames are carried forward in results
rownames(dune_trait_env$comm) <- dune_trait_env$comm$Sites

mod <- dc_CA(formulaEnv = ~A1 + Moist + Mag + Use + Manure,
             formulaTraits = ~ SLA + Height + LDMC + Seedmass + Lifespan,
             response = dune_trait_env$comm[, -1],  # must delete "Sites"
             dataEnv = dune_trait_env$envir,
             dataTraits = dune_trait_env$traits,
             verbose = FALSE)

env_scores <- scores(mod, display = "tval")

env_scores <- data.frame(env_scores)
env_scores$group <- c("quantitative", "category")[c(1, 1, 2, 2, 2, 1, 1)]                  
plot_species_scores_bk(
  species_scores = env_scores,
  ylab = "optimistic t-values",  threshold = 0,  y_lab_interval = 1,
  scoresname = "dcCA1", speciesgroup = "group", verbose = FALSE
)