plot_tax_pq: Plot taxonomic distribution in function of a factor with...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot taxonomic distribution in function of a factor with stacked bar in %

Description

An alternative to phyloseq::plot_bar() function.

Usage

plot_tax_pq(
  physeq,
  fact = NULL,
  merge_sample_by = NULL,
  type = "nb_seq",
  taxa_fill = "Order",
  print_values = TRUE,
  color_border = "lightgrey",
  linewidth = 0.1,
  prop_print_value = 0.01,
  nb_print_value = NULL,
  add_info = TRUE,
  na_remove = TRUE,
  clean_pq = TRUE
)

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.
merge_sample_by	a vector to determine which samples to merge using the merge_samples2() function. Need to be in physeq@sam_data
type	If "nb_seq" (default), the number of sequences is used in plot. If "nb_taxa", the number of ASV is plotted. If both, return a list of two plots, one for nbSeq and one for ASV.
taxa_fill	(default: 'Order'): Name of the taxonomic rank of interest
print_values	(logical, default TRUE): Do we print some values on plot?
color_border	color for the border
linewidth	The line width of geom_bar
prop_print_value	minimal proportion to print value (default 0.01)
nb_print_value	number of higher values to print (replace prop_print_value if both are set).
add_info	(logical, default TRUE) Do we add title and subtitle with information about the total number of sequences and the number of samples per modality.
na_remove	(logical, default TRUE) if TRUE remove all the samples with NA in the split_by variable of the physeq@sam_data slot
clean_pq	(logical) If set to TRUE, empty samples are discarded after subsetting ASV

Value

A ggplot2 graphic

Author(s)

Adrien Taudière

See Also

tax_bar_pq() and multitax_bar_pq()

Examples

data(data_fungi_sp_known)
plot_tax_pq(data_fungi_sp_known,
  "Time",
  merge_sample_by = "Time",
  taxa_fill = "Class"
)

plot_tax_pq(data_fungi_sp_known,
  "Height",
  merge_sample_by = "Height",
  taxa_fill = "Class",
  na_remove = TRUE,
  color_border = rgb(0, 0, 0, 0)
)

plot_tax_pq(data_fungi_sp_known,
  "Height",
  merge_sample_by = "Height",
  taxa_fill = "Class",
  na_remove = FALSE,
  clean_pq = FALSE
)

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