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Plot the distribution of sequences or ASV in one taxonomic levels

Source: R/plot_functions.R
tax_bar_pq.Rd

lifecycle-experimental

Graphical representation of distribution of taxonomy, optionnaly across a factor.

Usage

tax_bar_pq(
  physeq,
  fact = "Sample",
  taxa = "Order",
  percent_bar = FALSE,
  nb_seq = TRUE,
  add_ribbon = FALSE,
  ribbon_alpha = 0.3,
  label_taxa = FALSE,
  void_theme = TRUE,
  show_values = FALSE,
  minimum_value_to_show = 0,
  label_size = 3.2,
  value_size = 3,
  top_label_size = 3.2,
  bar_width = NULL,
  bar_internal_color = NA,
  linewidth_bar_internal = ifelse(is.na(bar_internal_color), 0, 0.5),
  show_n_samples = FALSE
)

Arguments

physeq

(required) a phyloseq-class object obtained using the phyloseq package.

fact

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

percent_bar

(default FALSE) If TRUE, the stacked bar fill all the space between 0 and 1. It just set position = "fill" in the ggplot2::geom_bar() function

nb_seq

(logical; default TRUE) If set to FALSE, only the number of ASV is count. Concretely, physeq otu_table is transformed in a binary otu_table (each value different from zero is set to one)

add_ribbon

(logical; default FALSE) If TRUE and fact is not "Sample", add curved ribbons connecting matching taxa between adjacent bars. Only meaningful when fact has more than one level.

ribbon_alpha

(numeric; default 0.3) Transparency of the ribbons.

label_taxa

(logical; default FALSE) If TRUE, replace the legend with direct labels on the right side of the last bar. Taxa that appear in the first bar but are absent from the last bar are additionally labelled on the left side of the first bar. Segments are drawn to resolve overlapping labels.

void_theme

(logical; default TRUE) If TRUE, use ggplot2::theme_void() when label_taxa is TRUE.

show_values

(logical; default FALSE) If TRUE, display abundance values (or percentages when percent_bar = TRUE) inside bar segments that exceed minimum_value_to_show.

minimum_value_to_show

(numeric; default 0) When show_values = TRUE, only segments with a value strictly above this threshold get a label.

label_size

(numeric; default 3.2) Font size (in ggplot2 mm units) for taxa labels when label_taxa = TRUE.

value_size

(numeric; default 3) Font size (in ggplot2 mm units) for value labels when show_values = TRUE.

top_label_size

(numeric; default 3.2) Font size (in ggplot2 mm units) for the top group labels when fact is not "Sample".

bar_width

(numeric; default NULL set 0.9 if add_ribbon = FALSE, 0.5 if add_ribbon = TRUE and fact != "Sample", and 0.6 if fact is only a one-level factor). Width of the bars. Set to 0 to have no visible bars and only ribbons.

bar_internal_color

(default NA) Color of bar borders. Use NA (default) to remove borders, which avoids thin white lines in PDF output. Set to e.g. "black" or "grey30" for visible borders.

linewidth_bar_internal

(default 0 if bar_internal_color is NA, otherwise 0.5) Line width of bar borders.

show_n_samples

(logical; default FALSE) If TRUE, the number of samples per group is displayed below the group label on the x-axis, as "group\n(n=X)".

Value

A ggplot2 plot with bar representing the number of sequence en each taxonomic groups

See also

plot_tax_pq() and multitax_bar_pq()

Author

Adrien Taudière

Examples


data_fungi_ab <- subset_taxa_pq(data_fungi,
  taxa_sums(data_fungi) > 10000)
#> Cleaning suppress 0 taxa (  ) and 15 sample(s) ( BE9-006-B_S27_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 1385
#> Number of kept ASV 35
#> Number of kept samples 170
tax_bar_pq(data_fungi_ab) + theme(legend.position = "none")

tax_bar_pq(data_fungi_ab, taxa = "Class", fact = "Height",
  show_n_samples = TRUE)

# \donttest{
tax_bar_pq(data_fungi_ab, taxa = "Class")

tax_bar_pq(data_fungi_ab, taxa = "Class", percent_bar = TRUE)

tax_bar_pq(data_fungi_ab, taxa = "Class", fact = "Time")

tax_bar_pq(data_fungi_ab,
  taxa = "Class", fact = "Time",
  percent_bar = TRUE, add_ribbon = TRUE
)

tax_bar_pq(data_fungi_ab,
  taxa = "Class", fact = "Time",
  percent_bar = TRUE, add_ribbon = TRUE, label_taxa = TRUE
)
#> Warning: 1 taxon/taxa only appear in intermediate levels and will not be labelled: Atractiellomycetes. Consider using label_taxa = FALSE.

tax_bar_pq(data_fungi_ab,
  taxa = "Class", fact = "Time",
  show_values = TRUE, minimum_value_to_show = 10000
)

tax_bar_pq(data_fungi_ab, fact = "Height", taxa = "Class",
  nb_seq = FALSE, percent_bar = TRUE, label_taxa = TRUE,
  add_ribbon = TRUE, value_size=7, ribbon_alpha = .6,
  show_values=TRUE, label_size = 4, top_label_size = 6,
  minimum_value_to_show=0.05) |>
  reorder_distinct_colors(alternate_lightness=TRUE)


tax_bar_pq(data_fungi_mini, fact = "Height", taxa = "Order",
  nb_seq = TRUE, percent_bar = TRUE, label_taxa = TRUE,
  add_ribbon = TRUE, value_size=5,
  ribbon_alpha = .6, show_values=TRUE,
  label_size = 4, top_label_size = 8,
  minimum_value_to_show=0.05, bar_width = NULL,
  linewidth_bar_internal = 0.1, bar_internal_color="black") |>
  reorder_distinct_colors(alternate_lightness=TRUE)

# }