Hill Diversities and Corresponding Accumulation Curves for phyloseq

Basically a wrapper of vegan::renyi() and vegan::renyiaccum() functions

Usage

hill_curves_pq(
  physeq,
  merge_sample_by = NULL,
  color_fac = NULL,
  hill_scales = c(0, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64, Inf),
  nperm = NULL,
  na_remove = TRUE,
  wrap_factor = TRUE,
  plot_legend = TRUE,
  linewidth = 2,
  size_point = 2,
  ...
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

merge_sample_by

a vector to determine which samples to merge using the merge_samples2() function. Need to be in physeq@sam_data

color_fac

(optional): The variable to color the barplot. For ex. same as fact. If merge_sample_by is set, color_fac must be nested in the merge_sample_by factor. See examples.

hill_scales

Scales of Rényi diversity.

nperm

(int Default NULL) If a integer is set to nperm, nperm permutation are computed to draw confidence interval for each curves. The function use vegan::renyi() if nperm is NULL and vegan::renyiaccum() else.

na_remove

(logical, default FALSE) If set to TRUE, remove samples with NA in the variables set in merge_sample_by. Not used if merge_sample_by is NULL.

wrap_factor

(logical, default TRUE) Do the plot is wrap by the factor

plot_legend

(logical, default TRUE) If set to FALSE, no legend are plotted.

linewidth

(int, default 2) The linewidth of lines.

size_point

(int, default 1) The size of the point.

...

Other arguments passed on to vegan::renyi() function or vegan::renyiaccum() if nperm is not NULL.

Value

A ggplot2 object

Details

This function is mainly a wrapper of the work of others. Please make a reference to vegan::renyi() or vegan::renyiaccum() functions

Author

Adrien Taudière

Examples

if (requireNamespace("vegan")) {
  hill_curves_pq(data_fungi_mini, merge_sample_by = "Time")
  hill_curves_pq(data_fungi_mini, color_fac = "Time", plot_legend = FALSE)
  hill_curves_pq(data_fungi_mini,
    color_fac = "Time", plot_legend = FALSE,
    nperm = 9, size_point = 1, linewidth = 0.5
  )

  hill_curves_pq(data_fungi_mini,
    nperm = 9, plot_legend = FALSE, size_point = 1,
    linewidth = 0.5
  )
  hill_curves_pq(data_fungi_mini, "Height",
    hill_scales = c(0, 1, 2, 8), plot_legend = FALSE
  )
  hill_curves_pq(data_fungi_mini, "Height",
    hill_scales = c(0, 0.5, 1, 2, 4, 8),
    nperm = 9
  )
  hill_curves_pq(data_fungi_mini, "Height", nperm = 9, wrap_factor = FALSE)

  data_fungi_mini@sam_data$H_T <- paste0(
    data_fungi_mini@sam_data$Height,
    "_", data_fungi_mini@sam_data$Time
  )
  merge_samples2(data_fungi_mini, "H_T")
  hill_curves_pq(data_fungi_mini, "H_T", color_fac = "Time", nperm = 9)
}
#> 17 were discarded due to NA in variables present in formula.
#> At least one sample name start with a zero.
#>     That can be a problem for some phyloseq functions such as
#>     plot_bar and psmelt.
#> Cleaning suppress 0 taxa and 0 samples.
#> Cleaning suppress 0 taxa and 0 samples.
#> Cleaning suppress 0 taxa and 0 samples.
#> Cleaning suppress 0 taxa and 0 samples.
#> 47 were discarded due to NA in variables present in formula.
#> Cleaning suppress 0 taxa and 0 samples.
#> 47 were discarded due to NA in variables present in formula.
#> Cleaning suppress 0 taxa and 0 samples.
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
#> 47 were discarded due to NA in variables present in formula.
#> Cleaning suppress 0 taxa and 0 samples.
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
#> Cleaning suppress 0 taxa and 0 samples.