ggscatt_pq: Scatterplot with marginal distributions and statistical...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Scatterplot with marginal distributions and statistical results against Hill diversity of phyloseq object

Description

Basically a wrapper of function ggstatsplot::ggscatterstats() for object of class phyloseq and Hill number.

Usage

ggscatt_pq(
  physeq,
  num_modality,
  hill_scales = c(0, 1, 2),
  rarefy_by_sample = FALSE,
  one_plot = TRUE,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
num_modality	(required) Name of the numeric column in physeq@sam_data to plot and test against hill numberk
hill_scales	(a vector of integer) The list of q values to compute the hill number H^q. If Null, no hill number are computed. Default value compute the Hill number 0 (Species richness), the Hill number 1 (exponential of Shannon Index) and the Hill number 2 (inverse of Simpson Index).
rarefy_by_sample	(logical, default FALSE) If TRUE, rarefy samples using phyloseq::rarefy_even_depth() function.
one_plot	(logical, default FALSE) If TRUE, return a unique plot with the three plot inside using the patchwork package.
...	Other arguments passed on to ggstatsplot::ggscatterstats() function.

Details

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

Value

Either an unique ggplot2 object (if one_plot is TRUE) or a list of ggplot2 plot for each hill_scales.

Author(s)

Adrien Taudière

See Also

ggbetween_pq()

Examples

if (requireNamespace("ggstatsplot")) {
  ggscatt_pq(data_fungi_mini, "Time", type = "non-parametric")
  ggscatt_pq(data_fungi_mini, "Time", hill_scales = 1:4, type = "parametric")
  ggscatt_pq(data_fungi_mini, "Sample_id",
    hill_scales = c(0, 0.5),
    one_plot = FALSE
  )
}

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.