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Venn diagram of shared taxa across sample groups

Source: R/simple_venn_pq.R
simple_venn_pq.Rd

lifecycle-experimental

Draws a Venn diagram showing shared and unique taxa (or higher-rank groups) across 2 to 4 levels of a sample variable, using only ggplot2 (no external Venn diagram package needed).

When taxonomic_rank is a character vector of length > 1 (the default), all ranks are displayed in a single combined figure using the patchwork package (must be installed). Set combine = FALSE to get a named list of individual plots instead.

For 2 and 3 groups, circles are used. For 4 groups, ellipses are used to ensure all intersection regions are representable.

Usage

simple_venn_pq(
  physeq,
  fact = NULL,
  min_nb_seq = 0,
  taxonomic_rank = c("Class", "Order", "Family", "Genus", "Species"),
  na_remove = TRUE,
  count_type = c("rank_taxa", "rank", "taxa", "sequences"),
  add_nb_samples = TRUE,
  fill_alpha = 0.3,
  border_size = 0.8,
  text_size = 4,
  scale_text = FALSE,
  hide_zero = TRUE,
  label_size = 4.5,
  colors = NULL,
  labels = NULL,
  show_na_count = FALSE,
  count_taxa = TRUE,
  match_by = c("refseq", "names"),
  combine = TRUE,
  verbose = TRUE
)

Arguments

physeq

(phyloseq or list_phyloseq, required) A phyloseq object, or a list_phyloseq object. When a list_phyloseq is provided, it is first merged into a single phyloseq using merge_lpq() (each original phyloseq becomes one sample) and the fact parameter is automatically set to "source_name".

fact

(character, required when physeq is a phyloseq) Name of a variable in sample_data(physeq) defining the groups (2-4 levels). Ignored when physeq is a list_phyloseq.

min_nb_seq

(integer, default 0) Minimum total read count for a taxon to be considered present in a group. A taxon must have strictly more than min_nb_seq reads in a group to be included.

taxonomic_rank

(character or NULL) Taxonomic rank(s) at which to aggregate (via phyloseq::tax_glom()) before computing the Venn diagram. Defaults to all standard ranks (Kingdom through Species). Use NULL to skip aggregation and work at ASV/OTU level.

na_remove

(logical, default TRUE) Remove samples with NA in fact and, when aggregating, taxa with NA at taxonomic_rank.

count_type

(character, default "rank_taxa") What to count in each Venn region. One of:

  • "rank": number of unique taxonomic levels (e.g. number of shared Classes). This is the default.

  • "taxa": number of ASVs/OTUs assigned to the shared taxonomic levels.

  • "sequences": total number of reads for ASVs/OTUs assigned to the shared taxonomic levels.

  • "rank_taxa": shows both rank and taxa counts as "nb_rank (nb_taxa)". Ignored when taxonomic_rank is NULL (ASV-level), where "rank" and "taxa" are equivalent.

add_nb_samples

(logical, default TRUE) Append sample count to group labels.

fill_alpha

(numeric, default 0.3) Fill transparency for shapes.

border_size

(numeric, default 0.8) Border line width.

text_size

(numeric, default 4) Base size of count labels inside regions.

scale_text

(logical, default FALSE) If TRUE, scale the size of count labels proportionally to the count value. The text_size parameter then acts as the base (minimum) size.

hide_zero

(logical, default TRUE) If TRUE, hide count labels that are zero (or "0 (0)" when count_type = "rank_taxa").

label_size

(numeric, default 4.5) Size of group name labels.

colors

(character or NULL) Vector of colors, one per group. Defaults to a 4-color qualitative palette.

labels

(character or NULL, default NULL) Custom labels for the groups, in the same order as the levels of fact (or the list_phyloseq names). Must have the same length as the number of groups. When NULL, the original level names are used. Not that the order is the one of the levels in fact.

show_na_count

(logical, default FALSE) If TRUE, display the number of taxa with NA at the chosen taxonomic_rank in the bottom-left corner of the plot. When count_type = "taxa", the sum of all Venn region counts plus the NA count equals ntaxa(physeq). Ignored when taxonomic_rank is NULL.

count_taxa

(logical, default TRUE) If TRUE, append a "Taxa" panel to the Venn diagram showing shared and unique individual taxa (ASVs/OTUs) alongside the aggregated taxonomic ranks. A temporary Taxa column is added to the tax_table with each taxon's name as its value. Ignored when taxonomic_rank is NULL.

match_by

(character, default "refseq") Passed to merge_lpq() when physeq is a list_phyloseq. One of "refseq" or "names".

combine

(logical, default TRUE) When taxonomic_rank has length > 1, combine plots into a single patchwork figure. Set to FALSE to return a named list of individual ggplot objects. Requires the patchwork package.

verbose

(logical, default TRUE) Print a message when no taxa meet the criteria.

Value

A ggplot2 object (single rank), a patchwork object (multiple ranks with combine = TRUE), or a named list of ggplot2 objects (multiple ranks with combine = FALSE).

Author

Adrien Taudiere

Examples

# Default: all ranks combined in one figure
simple_venn_pq(data_fungi_mini, "Height")


# At genus level only
simple_venn_pq(data_fungi_mini, "Height", taxonomic_rank = "Genus")


# Multiple ranks as a list
plots <- simple_venn_pq(
  data_fungi_mini, "Height",
  taxonomic_rank = c("Family", "Genus"),
  combine = FALSE
)
plots[["Family"]]


# Count ASVs instead of rank levels
simple_venn_pq(data_fungi_mini, "Height",
  taxonomic_rank = "Genus", count_type = "taxa"
)


# Scale text by count value
simple_venn_pq(data_fungi_mini, "Height",
  taxonomic_rank = "Genus", scale_text = TRUE
)


# From a list_phyloseq object
# Subset to the 80 most abundant taxa to keep the example fast
# (the full data_fungi has 1420 taxa).
data_fungi_small <- prune_taxa(
  names(sort(taxa_sums(data_fungi), decreasing = TRUE))[1:80],
  data_fungi
)
data_fungi_small <- clean_pq(prune_samples(
  sample_sums(data_fungi_small) >= 500, data_fungi_small
))
lpq <- list_phyloseq(list(
  fungi = data_fungi_mini,
  fungi2 = data_fungi_small
))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: EXPLORATION
#> ℹ 118 common samples, 43 common taxa
#> ✔ list_phyloseq created (EXPLORATION)
simple_venn_pq(lpq, taxonomic_rank = "Genus")
#> Merging 2 phyloseq objects by refseq: 45 + 80 taxa -> 82 unique sequences.


 simple_venn_pq(data_fungi_mini, "Height",
   taxonomic_rank = NULL,
   labels = c("Low alt.", "Mid alt.", "High alt.")
 )