Plot the partition the variation of a phyloseq object

Graphical representation of the partition of variation obtain with var_par_pq().

Usage

plot_var_part_pq(
  res_varpart,
  cutoff = 0,
  digits = 1,
  digits_quantile = 2,
  fill_bg = c("seagreen3", "mediumpurple", "blue", "orange"),
  show_quantiles = FALSE,
  filter_quantile_zero = TRUE,
  show_dbrda_signif = FALSE,
  show_dbrda_signif_pval = 0.05,
  alpha = 63,
  id.size = 1.2,
  min_prop_pval_signif_dbrda = 0.95
)

Arguments

res_varpart: (required) the result of the functions var_par_pq() or var_par_rarperm_pq()
cutoff: The values below cutoff will not be displayed.
digits: The number of significant digits.
digits_quantile: The number of significant digits for quantile.
fill_bg: Fill colours of ellipses.
show_quantiles: Do quantiles are printed ?
filter_quantile_zero: Do we filter out value with quantile encompassing the zero value?
show_dbrda_signif: Do dbrda significance for each component is printed using *?
show_dbrda_signif_pval: (float, [0:1]) The value under which the dbrda is considered significant.
alpha: (int, [0:255]) Transparency of the fill colour.
id.size: A numerical value giving the character expansion factor for the names of circles or ellipses.
min_prop_pval_signif_dbrda: (float, [0:1]) Only used if using the result of var_par_rarperm_pq() function. The * for dbrda_signif is only add if at least min_prop_pval_signif_dbrda of permutations show significance.

Value

A plot

Details

This function is mainly a wrapper of the work of others. Please make a reference to vegan::varpart() if you use this function.

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("vegan")) {
  data_fungi_woNA <- subset_samples(data_fungi, !is.na(Time) & !is.na(Height))
  res_var_9 <- var_par_rarperm_pq(
    data_fungi_woNA,
    list_component = list(
      "Time" = c("Time"),
      "Size" = c("Height", "Diameter")
    ),
    nperm = 9,
    dbrda_computation = TRUE
  )
  res_var_2 <- var_par_rarperm_pq(
    data_fungi_woNA,
    list_component = list(
      "Time" = c("Time"),
      "Size" = c("Height", "Diameter")
    ),
    nperm = 2,
    dbrda_computation = TRUE
  )
  res_var0 <- var_par_pq(data_fungi_woNA,
    list_component = list(
      "Time" = c("Time"),
      "Size" = c("Height", "Diameter")
    ),
    dbrda_computation = TRUE
  )
  plot_var_part_pq(res_var0, digits_quantile = 2, show_dbrda_signif = TRUE)
  plot_var_part_pq(res_var_9,
    digits_quantile = 2, show_quantiles = TRUE,
    show_dbrda_signif = TRUE
  )
  plot_var_part_pq(
    res_var_2,
    digits = 5,
    digits_quantile = 2,
    cutoff = 0,
    show_quantiles = TRUE
  )
}
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# }