plot_eha_log2: Plots an log2 spaced EHA spectra

In WaverideR: Extracting Signals from Wavelet Spectra

Plots an log2 spaced EHA spectra

Description

Plot wavelet scalogram using the outcome of the eha_log2 function.

Usage

plot_eha_log2(
  eha_log2 = NULL,
  plot_opt = "Amplitude",
  lowerPeriod = NULL,
  upperPeriod = NULL,
  n.levels = 100,
  palette_name = "rainbow",
  color_brewer = "grDevices",
  useRaster = TRUE,
  periodlab = "Period (metres)",
  x_lab = "depth (metres)",
  keep_editable = FALSE,
  dev_new = TRUE,
  plot_dir = TRUE,
  add_lines = NULL,
  add_points = NULL,
  add_abline_h = NULL,
  add_abline_v = NULL,
  add_MTM_peaks = FALSE,
  add_data = TRUE,
  add_avg = FALSE,
  pval_abline = c(0.1, 0.05),
  pval_cutoff = c(0.1),
  add_MTM = FALSE,
  mtm_siglvl = 0.95,
  demean_mtm = TRUE,
  detrend_mtm = TRUE,
  padfac_mtm = 5,
  tbw_mtm = 3,
  plot_horizontal = TRUE
)

Arguments

eha_log2	eha_log2 object created using the eha_log2 function.
plot_opt	plot options are "Power", "Amplitude", "Probability" or "F_test"
lowerPeriod	Lowest period value which will be plotted
upperPeriod	Highest period value which will be plotted
n.levels	Number of color levels Default=100.
palette_name	Name of the color palette which is used for plotting. The color palettes than can be chosen depends on which the R package is specified in the color_brewer parameter. The included R packages from which palettes can be chosen from are; the 'RColorBrewer', 'grDevices', 'ColorRamps' and 'Viridis' R packages. There are many options to choose from so please read the documentation of these packages Default=rainbow. The R package 'viridis' has the color palette options: “magma”, “plasma”, “inferno”, “viridis”, “mako”, and “rocket” and “turbo” To see the color palette options of the The R pacakge 'RColorBrewer' run the RColorBrewer::brewer.pal.info() function The R package 'colorRamps' has the color palette options:"blue2green", "blue2green2red", "blue2red", "blue2yellow", "colorRamps", "cyan2yellow", "green2red", "magenta2green", "matlab.like", "matlab.like2" and "ygobb" The R package 'grDevices' has the built in palette options:"rainbow", "heat.colors", "terrain.colors","topo.colors" and "cm.colors" To see even more color palette options of the The R pacakge 'grDevices' run the grDevices::hcl.pals() function The R package 'scico' has the color palette options: “acton”, “bam”,“bamako”, “bamO”, “batlow”, “batlowK”,“batlowW”,“berlin”,“bilbao”,”broc”,”brocO”, ”buda”,”bukavu”,”cork”,”CorkO”,”davos”,”devon”,”fes”,”Glasgow”,”grayC”, “hawaii”,”imola”,”lajolla”,”lapaz”,”lipari”,”lisbon”,”manague”,”navia”, ”nuuk”,”oleron”,”oslo”,”roma”,”romaO”,”Tofino”,”Tokyo”,”turku”,”Vanimo”, ”vik”,”vikO” The R package 'Viridis' has the color palette options: “magma”, “plasma”, “inferno”, “viridis”, “mako”, and “rocket” and “turbo”
color_brewer	Name of the R package from which the color palette is chosen from. The included R packages from which palettes can be chosen are; the RColorBrewer, grDevices, ColorRamps,scico and Viridis R packages. There are many options to choose from so please read the documentation of these packages. "Default=grDevices
useRaster	Plot as a raster or vector image Default=TRUE. WARNING plotting as a vector image is computationally intensive.
periodlab	Label for the y-axis Default="Period (metres)".
x_lab	Label for the x-axis Default="depth (metres)".
keep_editable	Keep option to add extra features after plotting Default=FALSE
dev_new	Opens a new plotting window to plot the plot, this guarantees a "nice" looking plot however when plotting in an R markdown document the plot might not plot Default=TRUE
plot_dir	The direction of the proxy record which is assumed for tuning if time increases with increasing depth/time values (e.g. bore hole data which gets older with increasing depth ) then plot_dir should be set to TRUE if time decreases with depth/time values (eg stratospheric logs where 0m is the bottom of the section) then plot_dir should be set to FALSE plot_dir=TRUE
add_lines	Add lines to the wavelet plot input should be matrix with first axis being depth/time the columns after that should be period values Default=NULL
add_points	Add points to the wavelet plot input should be matrix with first axis being depth/time and columns after that should be period values Default=NULL
add_abline_h	Add horizontal lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) Default=NULL
add_abline_v	Add vertical lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) Default=NULL
add_MTM_peaks	Add the MTM peak periods as horizontal lines Default=FALSE
add_data	Plot the data on top of the wavelet Default=TRUE
add_avg	Plot the average wavelet spectral power to the side of the wavelet Default=FALSE
pval_abline	p value of the abline
pval_cutoff	p value cutoff below which no data is displayed
add_MTM	Add the MTM plot next to the wavelet plot Default=FALSE
mtm_siglvl	select the significance level (0-1) for the MTM spectrum Default=0.95
demean_mtm	Remove mean from data before conducting the MTM analysis Default=TRUE
detrend_mtm	Remove mean from data before conducting the MTM analysis Default=TRUE
padfac_mtm	Pad factor for the MTM analysis Default=5
tbw_mtm	time bandwidth product of the MTM analysis Default=3
plot_horizontal	plot the wavelet horizontal or vertical eg y axis is depth or y axis power Default=TRUE

Value

The output is a plot of a EHA spectra. if add_MTM_peaks = TRUE then the output of the MTM analysis will given as matrix

Author(s)

Code based on the wt.image" functions of the 'WaveletComp' R package The EHA and MTM analysis parts are from the astrochron R package of Meyers et al., (2012)

References

Angi Roesch and Harald Schmidbauer (2018). WaveletComp: Computational Wavelet Analysis. R package version 1.1. https://CRAN.R-project.org/package=WaveletComp

S.R. Meyers, 2012, Seeing Red in Cyclic Stratigraphy: Spectral Noise Estimation for Astrochronology: Paleoceanography, 27, PA3228, <doi:10.1029/2012PA002307>

S.R. Meyers, 2019 Cyclostratigraphy and the problem of astrochronologic testing, Earth-Science Reviews, Volume 190, <doi.org/10.1016/j.earscirev.2018.11.015.>

Examples

#Example 1. A plot of a wavelet spectra using the Total Solar Irradiance
# data set of Steinhilber et al., (2012)

TSI_eha_log2 <- eha_log2(data = TSI,
win =  8192,
tbw = 4,
demean = TRUE,
detrend = TRUE,
upperPeriod = 8192,
lowerPeriod = 50,
pad = NULL,
padding = "noise")

plot_eha_log2(
eha_log2 = TSI_eha_log2,
plot_opt = "Amplitude",
lowerPeriod = 50,
upperPeriod = 8192,
n.levels = 100,
palette_name = "rainbow",
color_brewer = "grDevices",
useRaster = TRUE,
periodlab = "Period (metres)",
x_lab = "depth (metres)",
keep_editable = FALSE,
dev_new = TRUE,
plot_dir = TRUE,
add_lines = NULL,
add_points = NULL,
add_abline_h = NULL,
add_abline_v = NULL,
add_MTM_peaks = FALSE,
add_data = TRUE,
add_avg = FALSE,
add_MTM = FALSE,
mtm_siglvl = 0.95,
demean_mtm = TRUE,
detrend_mtm = TRUE,
padfac_mtm = 5,
tbw_mtm = 3,
plot_horizontal = TRUE)

#Example 2. A plot of a wavelet spectra using the magnetic susceptibility
#data set of Pas et al., (2018)
mag_eha_log2 <- eha_log2(data = mag,
win =  50,
tbw = 4,
demean = TRUE,
detrend = TRUE,
upperPeriod = 50,
lowerPeriod = 1,
pad = NULL,
padding = "noise")

plot_eha_log2(
eha_log2 = mag_eha_log2,
plot_opt = "Amplitude",
lowerPeriod = 1,
upperPeriod = 50,
n.levels = 100,
palette_name = "rainbow",
color_brewer = "grDevices",
useRaster = TRUE,
periodlab = "Period (metres)",
x_lab = "depth (metres)",
keep_editable = FALSE,
dev_new = TRUE,
plot_dir = TRUE,
add_lines = NULL,
add_points = NULL,
add_abline_h = NULL,
add_abline_v = NULL,
add_MTM_peaks = FALSE,
add_data = TRUE,
add_avg = FALSE,
add_MTM = FALSE,
mtm_siglvl = 0.95,
demean_mtm = TRUE,
detrend_mtm = TRUE,
padfac_mtm = 5,
tbw_mtm = 3,
plot_horizontal = TRUE)


#Example 3. A plot of a wavelet spectra using the greyscale
# data set of Zeeden et al., (2013)
grey_eha_log2 <- eha_log2(data = grey,
win =  20,
tbw = 4,
demean = TRUE,
detrend = TRUE,
upperPeriod = 20,
lowerPeriod = 1,
pad = NULL,
padding = "noise")


plot_eha_log2(
eha_log2 = grey_eha_log2,
plot_opt = "Amplitude",
lowerPeriod = 1,
upperPeriod = 20,
n.levels = 100,
palette_name = "rainbow",
color_brewer = "grDevices",
useRaster = TRUE,
periodlab = "Period (metres)",
x_lab = "depth (metres)",
keep_editable = FALSE,
dev_new = TRUE,
plot_dir = TRUE,
add_lines = NULL,
add_points = NULL,
add_abline_h = NULL,
add_abline_v = NULL,
add_MTM_peaks = FALSE,
add_data = TRUE,
add_avg = FALSE,
add_MTM = FALSE,
mtm_siglvl = 0.95,
demean_mtm = TRUE,
detrend_mtm = TRUE,
padfac_mtm = 5,
tbw_mtm = 3,
plot_horizontal = TRUE)

WaverideR documentation built on April 6, 2026, 5:06 p.m.