ggvenn_pq: Venn diagram of 'phyloseq-class' object using...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Venn diagram of phyloseq-class object using ggVennDiagram::ggVennDiagram function

Description

Note that you can use ggplot2 function to customize the plot for ex. + scale_fill_distiller(palette = "BuPu", direction = 1) and + scale_x_continuous(expand = expansion(mult = 0.5)). See examples.

Usage

ggvenn_pq(
  physeq = NULL,
  fact = NULL,
  min_nb_seq = 0,
  taxonomic_rank = NULL,
  split_by = NULL,
  add_nb_samples = TRUE,
  add_nb_seq = FALSE,
  rarefy_before_merging = FALSE,
  rarefy_after_merging = FALSE,
  return_data_for_venn = FALSE,
  verbose = TRUE,
  type = "nb_taxa",
  na_remove = TRUE,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required): Name of the factor to cluster samples by modalities. Need to be in physeq@sam_data.
min_nb_seq	minimum number of sequences by OTUs by samples to take into count this OTUs in this sample. For example, if min_nb_seq=2,each value of 2 or less in the OTU table will not count in the venn diagram
taxonomic_rank	Name (or number) of a taxonomic rank to count. If set to Null (the default) the number of OTUs is counted.
split_by	Split into multiple plot using variable split_by. The name of a variable must be present in sam_data slot of the physeq object.
add_nb_samples	(logical, default TRUE) Add the number of samples to levels names
add_nb_seq	(logical, default FALSE) Add the number of sequences to levels names
rarefy_before_merging	Rarefy each sample before merging by the modalities of args fact. Use phyloseq::rarefy_even_depth() function
rarefy_after_merging	Rarefy each sample after merging by the modalities of args fact.
return_data_for_venn	(logical, default FALSE) If TRUE, the plot is not returned, but the resulting dataframe to plot with ggVennDiagram package is returned.
verbose	(logical, default TRUE) If TRUE, prompt some messages.
type	If "nb_taxa" (default), the number of taxa (ASV, OTU or taxonomic_rank if taxonomic_rank is not NULL) is used in plot. If "nb_seq", the number of sequences is plotted. taxonomic_rank is never used if type = "nb_seq".
na_remove	(logical, default TRUE) If set to TRUE, remove samples with NA in the variables set in fact param
...	Other arguments for the ggVennDiagram::ggVennDiagram function for ex. category.names.

Value

A ggplot2 plot representing Venn diagram of modalities of the argument factor or if split_by is set a list of plots.

Author(s)

Adrien Taudière

See Also

upset_pq()

Examples

if (requireNamespace("ggVennDiagram")) {
  ggvenn_pq(data_fungi, fact = "Height")
}

if (requireNamespace("ggVennDiagram")) {
  ggvenn_pq(data_fungi, fact = "Height") +
    ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1)
  pl <- ggvenn_pq(data_fungi, fact = "Height", split_by = "Time")
  for (i in seq_along(pl)) {
    p <- pl[[i]] +
      scale_fill_distiller(palette = "BuPu", direction = 1) +
      theme(plot.title = element_text(hjust = 0.5, size = 22))
    print(p)
  }

  data_fungi2 <- subset_samples(data_fungi, data_fungi@sam_data$Tree_name == "A10-005" |
    data_fungi@sam_data$Height %in% c("Low", "High"))
  ggvenn_pq(data_fungi2, fact = "Height")

  ggvenn_pq(data_fungi2, fact = "Height", type = "nb_seq")

  ggvenn_pq(data_fungi, fact = "Height", add_nb_seq = TRUE, set_size = 4)
  ggvenn_pq(data_fungi, fact = "Height", rarefy_before_merging = TRUE)
  ggvenn_pq(data_fungi, fact = "Height", rarefy_after_merging = TRUE) +
    scale_x_continuous(expand = expansion(mult = 0.5))

  # For more flexibility, you can save the dataset for more precise construction
  # with ggplot2 and ggVennDiagramm
  # (https://gaospecial.github.io/ggVennDiagram/articles/fully-customed.html)
  res_venn <- ggvenn_pq(data_fungi, fact = "Height", return_data_for_venn = TRUE)

  ggplot() +
    # 1. region count layer
    geom_polygon(aes(X, Y, group = id, fill = name),
      data = ggVennDiagram::venn_regionedge(res_venn)
    ) +
    scale_fill_manual(values = funky_color(7)) +
    # 2. set edge layer
    geom_path(aes(X, Y, color = id, group = id),
      data = ggVennDiagram::venn_setedge(res_venn),
      show.legend = FALSE, linewidth = 2
    ) +
    scale_color_manual(values = c("red", "red", "blue")) +
    # 3. set label layer
    geom_text(aes(X, Y, label = name),
      data = ggVennDiagram::venn_setlabel(res_venn)
    ) +
    # 4. region label layer
    geom_label(
      aes(X, Y, label = paste0(
        count, " (",
        scales::percent(count / sum(count), accuracy = 2), ")"
      )),
      data = ggVennDiagram::venn_regionlabel(res_venn)
    ) +
    theme_void()
}

adrientaudiere/MiscMetabar documentation built on Dec. 19, 2024, 3:16 a.m.