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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,
  alpha.line = 1,
  alpha.ribbon = 0.3,
  removeFirst = 0,
  removeLast = 0,
  force.CI = FALSE,
  min.colours = 2
)

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

Colour or name of variable to which to map to colour

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. Will be unpredictable when used with a list of spectra, or spec_df object with multiple spectra with different frequency axes.

force.CI

Force the plotting of confidence regions when the total number of frequencies exceeds 10000. Defaults to FALSE

min.colours

minimum number of spectra before starting to colour them separately

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)
#> Warning: Time series is not a ts object and deltat is not set. Frequency array and axes may be incorrect.
sp1 <- AddConfInterval(sp1)
sp2 <- SpecMTM(ts2)
#> Warning: Time series is not a ts object and deltat is not set. Frequency array and axes may be incorrect.

# 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