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Plot accumulation curves for phyloseq-class object

Source: R/plot_functions.R
accu_plot.Rd

lifecycle-maturing

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.

See also

specaccum accu_samp_threshold()

Author

Adrien Taudière

Examples

# \donttest{
data("GlobalPatterns", package = "phyloseq")
GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
GP <- rarefy_even_depth(subset_samples_pq(GP, sample_sums(GP) > 3000))
#> You set `rngseed` to FALSE. Make sure you've set & recorded
#>  the random seed of your session for reproducibility.
#> See `?set.seed`
#> ...
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
#> 60OTUs were removed because they are no longer 
#> present in any sample after random subsampling
#> ...
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’
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)
#> Warning: no non-missing arguments to max; returning -Inf

p + theme(legend.position = "none")
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_line()`).


p + xlim(c(0, 400))
#> Warning: Removed 3256 rows containing missing values or values outside the scale range
#> (`geom_line()`).

# }