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Plot One or More Spectra with ggplot2

gg_spec.Rd

Plot One or More Spectra with ggplot2

Usage

gg_spec(
  x,
  gg = NULL,
  conf = TRUE,
  spec_id = NULL,
  colour = spec_id,
  group = spec_id,
  linetype = NULL,
  alpha.line = 1,
  alpha.ribbon = c(0.166, 0.333),
  removeFirst = 0,
  removeLast = 0,
  min.colours = 2,
  force.lims = FALSE,
  force.CI = NULL,
  quantiles = FALSE,
  time_unit = NULL
)

Arguments

x

An object of class "spec" or "spec_df"

gg

An existing ggplot object on which to add a new spec layer

conf

Plot shaded confidence interval if it exists in the spec object

spec_id

Name for this plot layer

colour

Name of variable map to colour, unquoted

group

Name of variable to map to group, unquoted

linetype

Name of variable map to linetype, unquoted

alpha.line

Alpha level for the spectra line(s)

alpha.ribbon

Alpha level for the confidence region(s)

removeFirst, removeLast

Remove first or last "n" values on the low or high frequency side respectively. Operates on a per group basis.

min.colours

Minimum number of spectra before starting to colour them separately

force.lims, force.CI

Force the plotting of confidence regions when the total number of frequencies exceeds 10000. force.CI is deprecated, use force.lims. Defaults to FALSE

quantiles

Plot uncertainty quantiles if they exist in the spec object

time_unit

Optional string giving the time unit for axes labels, e.g. "years"

Value

a ggplot object

See also

Other functions to plot power spectra: LLines(), LPlot()

Examples

library(PaleoSpec)
N <- 1e03
beta <- 1
alpha <- 0.1

ts1 <- SimPLS(N = N, b = beta, a = alpha)
ts2 <- SimPLS(N = N, b = beta, a = alpha)
sp1 <- SpecMTM(ts1, deltat = 1)
sp1 <- AddConfInterval(sp1)
sp2 <- SpecMTM(ts2, deltat = 1)

# plot single spectrum
p <- gg_spec(sp1, spec_id = "df1")
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
p


# Add additional second spectra
p <- gg_spec(sp2, p, spec_id = "df2", removeFirst = 2)
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for alpha is already present.
#> Adding another scale for alpha, which will replace the existing scale.
p


p <- gg_spec(sp1, p, spec_id = "df3", removeLast = 200)
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for alpha is already present.
#> Adding another scale for alpha, which will replace the existing scale.
p


sp2 <- LogSmooth(sp1)
p <- gg_spec(sp1, spec_id = "df1")
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
p <- gg_spec(sp2, p, spec_id = "df2")
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for alpha is already present.
#> Adding another scale for alpha, which will replace the existing scale.
p <- p + ggplot2::geom_abline(intercept = log10(alpha), slope = -beta, colour = "red")
p


# Or directly plot named or unnamed list

gg_spec(list(sp1, sp2))

gg_spec(list(raw = sp1, smoothed = sp2))


# without setting any names all spectra will be black
p <- gg_spec(sp1)
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
sp2 <- LogSmooth(sp1)
p <- gg_spec(sp2, p)
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for alpha is already present.
#> Adding another scale for alpha, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
p