accu_plot: Plot accumulation curves for 'phyloseq-class' object

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot accumulation curves for phyloseq-class object

Description

Note that as most bioinformatic pipeline discard singleton, accumulation curves from metabarcoding cannot be interpreted in the same way as with conventional biodiversity sampling techniques.

Usage

accu_plot(
  physeq,
  fact = NULL,
  add_nb_seq = TRUE,
  step = NULL,
  by.fact = FALSE,
  ci_col = NULL,
  col = NULL,
  lwd = 3,
  leg = TRUE,
  print_sam_names = FALSE,
  ci = 2,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required) Name of the factor in physeq@sam_data used to plot different lines
add_nb_seq	(default: TRUE, logical) Either plot accumulation curves using sequences or using samples
step	(Integer) distance among points calculated to plot lines. A low value give better plot but is more time consuming. Only used if add_nb_seq = TRUE.
by.fact	(default: FALSE, logical) First merge the OTU table by factor to plot only one line by factor
ci_col	Color vector for confidence interval. Only use if add_nb_seq = FALSE. If add_nb_seq = TRUE, you can use ggplot to modify the plot.
col	Color vector for lines. Only use if add_nb_seq = FALSE. If add_nb_seq = TRUE, you can use ggplot to modify the plot.
lwd	(default: 3) thickness for lines. Only use if add_nb_seq = FALSE.
leg	(default: TRUE, logical) Plot legend or not. Only use if add_nb_seq = FALSE.
print_sam_names	(default: FALSE, logical) Print samples names or not? Only use if add_nb_seq = TRUE.
ci	(default: 2, integer) Confidence interval value used to multiply the standard error to plot confidence interval
...	Additional arguments passed on to ggplot if add_nb_seq = TRUE or to plot if add_nb_seq = FALSE

Value

A ggplot2 plot representing the richness accumulation plot if add_nb_seq = TRUE, else, if add_nb_seq = FALSE return a base plot.

Author(s)

Adrien Taudière

See Also

specaccum accu_samp_threshold()

Examples

data("GlobalPatterns", package = "phyloseq")
GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
GP <- rarefy_even_depth(subset_samples_pq(GP, sample_sums(GP) > 3000))
p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, by.fact = TRUE, step = 10)
p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, step = 10)

p + theme(legend.position = "none")

p + xlim(c(0, 400))

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