Skip to contents

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", "sequences", "rank_taxa"),
  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,
  show_na_count = FALSE,
  count_taxa = TRUE,
  match_by = c("refseq", "names"),
  combine = TRUE,
  verbose = TRUE,
  .lpq_n_samples = NULL
)

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") 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.

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
lpq <- list_phyloseq(list(
  fungi = data_fungi_mini,
  fungi2 = data_fungi
))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: NESTED_ROBUSTNESS
#> ℹ 137 common samples, 45 common taxa
#> ✔ list_phyloseq created (NESTED_ROBUSTNESS)
simple_venn_pq(lpq, taxonomic_rank = "Genus", count_taxa)
#> Merging 2 phyloseq objects by refseq: 45 + 1420 taxa -> 1420 unique sequences.