circle_pq: Plot OTU circle for 'phyloseq-class' object

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot OTU circle for phyloseq-class object

Description

Graphical representation of distribution of taxa across a factor.

Usage

circle_pq(
  physeq = NULL,
  fact = NULL,
  taxa = "Order",
  nproc = 1,
  add_nb_seq = TRUE,
  rarefy = FALSE,
  min_prop_tax = 0.01,
  min_prop_mod = 0.1,
  gap_degree = NULL,
  start_degree = NULL,
  row_col = NULL,
  grid_col = NULL,
  log10trans = FALSE,
  ...
)

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.
taxa	(default: 'Order') Name of the taxonomic rank of interest
nproc	(default 1) Set to number of cpus/processors to use for parallelization
add_nb_seq	(default: TRUE) Represent the number of sequences or the number of OTUs (add_nb_seq = FALSE)
rarefy	(logical) Does each samples modalities need to be rarefy in order to compare them with the same amount of sequences?
min_prop_tax	(default: 0.01) The minimum proportion for taxa to be plotted
min_prop_mod	(default: 0.1) The minimum proportion for modalities to be plotted
gap_degree	Gap between two neighbour sectors. It can be a single value or a vector. If it is a vector, the first value corresponds to the gap after the first sector.
start_degree	The starting degree from which the circle begins to draw. Note this degree is measured in the standard polar coordinate which means it is always reverse-clockwise.
row_col	Color vector for row
grid_col	Grid colors which correspond to sectors. The length of the vector should be either 1 or the number of sectors. It's preferred that grid_col is a named vector of which names correspond to sectors. If it is not a named vector, the order of grid_col corresponds to order of sectors.
log10trans	(logical) Should sequence be log10 transformed (more precisely by log10(1+x))?
...	Additional arguments passed on to chordDiagram or circos.par

Value

A chordDiagram plot representing the distribution of OTUs or sequences in the different modalities of the factor fact

Author(s)

Adrien Taudière

See Also

chordDiagram

circos.par

Examples

if (requireNamespace("pbapply")) {
  data("GlobalPatterns", package = "phyloseq")
  GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
  circle_pq(GP, "SampleType")
  circle_pq(GP, "SampleType", add_nb_seq = FALSE)
  circle_pq(GP, "SampleType", taxa = "Class")
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.