plot.Nonpareil.Curve {Nonpareil}

Plot a Nonpareil.Curve object.

Description

Plot a Nonpareil.Curve object.

Usage

## S3 method for class 'Nonpareil.Curve'
plot(
  x,
  col = NA,
  add = FALSE,
  new = !add,
  plot.observed = TRUE,
  plot.model = TRUE,
  plot.dispersion = FALSE,
  plot.diversity = TRUE,
  xlim = c(1000, 1e+13),
  ylim = c(1e-06, 1),
  main = paste("Nonpareil Curve for", x$label),
  xlab = "Sequencing effort (bp)",
  ylab = "Estimated Average Coverage",
  curve.lwd = 2,
  curve.alpha = 0.4,
  model.lwd = 1,
  model.alpha = 1,
  log = "x",
  arrow.length = 0.05,
  arrow.head = arrow.length,
  ...
)

Arguments

x

Nonpareil.Curve object to plot.

col

Color of the curve. If passed, it overrides the colors set in the Nonpareil.Curve object.

add

If TRUE, it attempts to use a previous (active) canvas to plot the curve.

new

Inverse of 'add'.

plot.observed

Indicates if the observed (rarefied) coverage is to be plotted.

plot.model

Indicates if the fitted model is to be plotted.

plot.dispersion

Indicates if (and how) dispersion of the replicates should be plotted. Supported values are:

• FALSE: no dispersion is plotted (default),

• 'sd': one standard deviation around the mean,

• 'ci95': 95

• 'ci90': 90

• 'ci50': 50

• 'iq': Inter-quartile range.

plot.diversity

If TRUE, the diversity estimate is plotted as a small arrow below the Nonpareil curve.

xlim

Limits of the sequencing effort (X-axis).

ylim

Limits of the coverage (Y-axis).

main

Title of the plot.

xlab

Label of the X-axis.

ylab

Label of the Y-axis.

curve.lwd

Line width of the rarefied coverage.

curve.alpha

Alpha value (from 0 to 1) of the rarefied coverage.

model.lwd

Line width of the model.

model.alpha

Alpha value (from 0 to 1) of the model.

log

Axis to plot in logarithmic scale. Supported values are:

• 'x': sequencing effort (default),

• 'y': coverage,

• 'xy': both logarithmic, or

• '': both linear.

arrow.length

If plot.diversity = TRUE, it determines the length of the arrow to display the divsersity (as a fraction of the ylim range).

arrow.head

If plot.diversity = TRUE, it determines the length of the arrow head to display the diversity index (in inches).

...

Additional graphical parameters.

Value

Retuns invisibly a Nonpareil.Curve object (same as x input). For additional details see help for summary.Nonpareil.Curve.