plot_wavelet_coherence: Plots a cross wavelet scalogram

In WaverideR: Extracting Signals from Wavelet Spectra

Plots a cross wavelet scalogram

Description

Plot cross wavelet scalogram using the outcome of the analyze_wavelet_coherence function.

Usage

plot_wavelet_coherence(
  wavelet_coh = NULL,
  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,
  plot_arrows = TRUE,
  pwr_quant = 0.85,
  n_arrows = 75,
  T_unit = 15,
  P_unit = 0.5,
  arrow_length = 0.075,
  arrow_lwd = 1.9,
  arrow_angle = 25,
  add_lines = NULL,
  add_points = NULL,
  add_abline_h = NULL,
  add_abline_v = NULL,
  add_data = TRUE,
  add_avg = FALSE,
  plot_horizontal = TRUE
)

Arguments

wavelet_coh	wavelet_coh object created using the analyze_wavelet_coherence function.
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
plot_arrows	add the phase arrows of the cross superlet transform Default=TRUE
pwr_quant	Power quantile above which the arrows are plotted Default= 0.85
n_arrows	number arrows width wise plotted on the time axis Default= 50
T_unit	length of the arrows in time units Default= 15
P_unit	length of the arrows in period units Default = 0.5
arrow_length	length of the slanted part of the arrow Default= 0.1
arrow_lwd	thickness of the arrow Default= 2
arrow_angle	angle of the slanted part of the arrow Default= 25
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_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
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 cross wavelet scalogram.

Author(s)

plotting code based on the "wt.image" and "analyze.coherency" functions of the 'WaveletComp' R package

References

Roesch, A., & Schmidbauer, H. (2018). WaveletComp: Computational Wavelet Analysis. R package version 1.1. https://CRAN.R-project.org/package=WaveletComp

Moca, V. V., Bârzan, H., Nagy-Dăbâcan, A., & Mureșan, R. C. (2021). Time-frequency super-resolution with superlets. Nature Communications, 12(1), 337. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41467-020-20539-9")}

Examples

#Example 1. A cross superlet plot of two etp solutions with noise overprint


etp_1 <- astrochron::etp(
 tmin = 0,
 tmax = 1500,
 dt = 1,
 eWt = 1.5,
 oWt = 0.75,
 pWt = 1,
 esinw = TRUE,
 standardize = TRUE,
 genplot = FALSE,
 verbose = FALSE
)

etp_2 <- astrochron::etp(
 tmin = 0,
 tmax = 1500,
 dt = 1,
 eWt = 1,
 oWt = 0.5,
 pWt = 1.5,
 esinw = TRUE,
 standardize = TRUE,
 genplot = FALSE,
verbose = FALSE
)

etp_1[, 2] <- etp_1[, 2] + colorednoise::colored_noise(
 nrow(etp_1),
 sd = sd(etp_1[, 2]) / 1.5,
 mean = mean(etp_1[, 2]),
 phi = 0.9
)
etp_2[, 2] <- etp_2[, 2] + colorednoise::colored_noise(
 nrow(etp_2),
 sd = sd(etp_2[, 2]) / 1.5,
 mean = mean(etp_2[, 2]),
 phi = 0.9
)

coh_etp <- analyze_wavelet_coherence(
 data_1 = etp_1,
 data_2  = etp_2,
 upperPeriod = 1024,
 lowerPeriod = 2
)
plot_wavelet_coherence(wavelet_coh = coh_etp, lowerPeriod = 2, upperPeriod = 1024,
              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,
              plot_arrows = TRUE,
              pwr_quant = 0.85,
              n_arrows = 50,
              T_unit = 15,
              P_unit  = 0.5,
              arrow_length = 0.1,
              arrow_lwd = 2,
              arrow_angle = 25,add_lines = NULL, add_points = NULL, add_abline_h = NULL,
              add_abline_v = NULL, add_data = TRUE, add_avg = FALSE, plot_horizontal = TRUE)

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