Alluvial plot for taxonomy and samples factor vizualisation

Basically a wrapper of ggalluvial package

Usage

ggaluv_pq(
  physeq,
  taxa_ranks = c("Phylum", "Class", "Order", "Family"),
  wrap_factor = NULL,
  by_sample = FALSE,
  rarefy_by_sample = FALSE,
  fact = NULL,
  type = "nb_seq",
  width = 1.2,
  min.size = 3,
  na_remove = FALSE,
  use_ggfittext = FALSE,
  use_geom_label = FALSE,
  size_lab = 2,
  ...
)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
taxa_ranks: A vector of taxonomic ranks. For examples c("Family","Genus"). If taxa ranks is not set (default value = c("Phylum", "Class", "Order", "Family")).
wrap_factor: A name to determine which samples to merge using merge_samples2() function. Need to be in physeq@sam_data. Need to be use when you want to wrap by factor the final plot with the number of taxa (type="nb_taxa")
by_sample: (logical) If FALSE (default), sample information is not taking into account, so the taxonomy is studied globally. If fact is not NULL, by_sample is automatically set to TRUE.
rarefy_by_sample: (logical, default FALSE) If TRUE, rarefy samples using phyloseq::rarefy_even_depth() function.
fact: (required) Name of the factor in physeq@sam_data used to plot the last column
type: If "nb_seq" (default), the number of sequences is used in plot. If "nb_taxa", the number of ASV is plotted.
width: (passed on to ggalluvial::geom_flow()) the width of each stratum, as a proportion of the distance between axes. Defaults to 1/3.
min.size: (passed on to ggfittext::geom_fit_text()) Minimum font size, in points. Text that would need to be shrunk below this size to fit the box will be hidden. Defaults to 4 pt.
na_remove: (logical, default FALSE) If set to TRUE, remove samples with NA in the variables set in formula.
use_ggfittext: (logical, default FALSE) Do we use ggfittext to plot labels?
use_geom_label: (logical, default FALSE) Do we use geom_label to plot labels?
size_lab: Size for label if use_ggfittext is FALSE
...: Other arguments passed on to ggalluvial::geom_flow() function.

Value

A ggplot object

Details

This function is mainly a wrapper of the work of others. Please make a reference to ggalluvial package if you use this function.

Author

Adrien Taudière

Examples

if (requireNamespace("ggalluvial")) {
  ggaluv_pq(data_fungi_mini)
}
#> Loading required namespace: ggalluvial

# \donttest{
if (requireNamespace("ggalluvial")) {
  ggaluv_pq(data_fungi_mini, type = "nb_taxa")

  ggaluv_pq(data_fungi_mini, wrap_factor = "Height", by_sample = TRUE, type = "nb_taxa") +
    facet_wrap("Height")

  ggaluv_pq(data_fungi_mini,
    width = 0.9, min.size = 10,
    type = "nb_taxa", taxa_ranks = c("Phylum", "Class", "Order", "Family", "Genus")
  ) +
    coord_flip() + scale_x_discrete(limits = rev)
}
#> Warning: `group` has missing values; corresponding samples will be dropped

# }