plot.Nonpareil.Curve: Plot a 'Nonpareil.Curve' object.

In Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'

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.

Nonpareil documentation built on Jan. 29, 2022, 1:08 a.m.