Nonpareil.set {Nonpareil}

Generates a collection of Nonpareil curves (a Nonpareil.Set object) and (optionally) plots all of them in a single canvas.

Description

Generates a collection of Nonpareil curves (a Nonpareil.Set object) and (optionally) plots all of them in a single canvas.

Usage

Nonpareil.set(
  files,
  col = NA,
  labels = NA,
  plot = TRUE,
  plot.opts = list(),
  ...
)

Arguments

files

Vector with the paths to the .npo files.

col

Color of the curves (vector). If not passed, values are randomly assigned. Values are recycled.

labels

Labels of the curves (vector). If not passed, values are determined by the filename. Values are recycled.

plot

If TRUE, it generates the Nonpareil curve plots.

plot.opts

Any parameters accepted by plot.Nonpareil.Set as a list.

...

Any additional parameters accepted by Nonpareil.curve.

Value

Returns invisibly a Nonpareil.Set object.

Examples

# Generate a Nonpareil plot with multiple curves
files <- system.file(
  "extdata",
  c("HumanGut.npo", "LakeLanier.npo", "IowaSoil.npo"),
  package = "Nonpareil"
)
col <- c("orange","darkcyan","firebrick4")
nps <- Nonpareil.set(
  files, col = col,
  plot.opts = list(plot.observed = FALSE, model.lwd = 2)
)

# Show the estimated values
print(nps)

# Show current coverage (as %)
summary(nps)[, "C"] * 100

# Extract Nd diversity index
summary(nps)[, "diversity"]

# Extract sequencing effort for nearly complete coverage (in Gbp)
summary(nps)[, "LRstar"] / 1e9

# Predict coverage for a sequencing effort of 10Gbp
sapply(nps$np.curves, predict, 10e9)