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Plot OTU circle for phyloseq-class object

Source: R/plot_functions.R
circle_pq.Rd

[Maturing]

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 taxon 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

See also

chordDiagram

circos.par

Author

Adrien Taudière

Examples

# \donttest{
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")
}
#> Loading required namespace: pbapply
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Only 4 modalities are plot (44.44%). Use 'min_prop_mod' to plot more samples.
#> Only 5 taxa are plot (45.45%). Use 'min_prop_tax' to plot more taxa
#> Only 4 modalities are plot (44.44%). Use 'min_prop_mod' to plot more samples.
#> Only 9 taxa are plot (81.82%). Use 'min_prop_tax' to plot more taxa

#> Only 4 modalities are plot (44.44%). Use 'min_prop_mod' to plot more samples.
#> Only 4 taxa are plot (44.44%). Use 'min_prop_tax' to plot more taxa


# }