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R/plot_Awavelet.R
In WaverideR: Extracting Signals from Wavelet Spectra
Defines functions
plot_Awavelet
Documented in
plot_Awavelet
#' @title Plots a adaptive wavelet scalogram
#'
#' @description Plot adaptive wavelet scalogram using the outcome of the \code{\link{analyze_Awavelet}} function.
#'
#'@param Awavelet wavelet object created using the \code{\link{analyze_Awavelet}} function.
#'@param lowerPeriod Lowest period value which will be plotted
#'@param upperPeriod Highest period value which will be plotted
#'@param n.levels Number of color levels \code{Default=100}.
#'@param 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 \code{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”
#'@param 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. "\code{Default=grDevices}
#'@param useRaster Plot as a raster or vector image \code{Default=TRUE}.
#'WARNING plotting as a vector image is computationally intensive.
#'@param periodlab Label for the y-axis \code{Default="Period (metres)"}.
#'@param x_lab Label for the x-axis \code{Default="depth (metres)"}.
#'@param keep_editable Keep option to add extra features after plotting \code{Default=FALSE}
#'@param 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 \code{Default=TRUE}
#'@param 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 \code{plot_dir=TRUE}
#'@param 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 \code{Default=NULL}
#'@param 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 \code{Default=NULL}
#'@param add_abline_h Add horizontal lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) \code{Default=NULL}
#'@param add_abline_v Add vertical lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) \code{Default=NULL}
#'@param add_MTM_peaks Add the MTM peak periods as horizontal lines \code{Default=FALSE}
#'@param add_data Plot the data on top of the wavelet \code{Default=TRUE}
#'@param add_avg Plot the average wavelet spectral power to the side of the wavelet \code{Default=FALSE}
#'@param add_MTM Add the MTM plot next to the wavelet plot \code{Default=FALSE}
#'@param mtm_siglvl select the significance level (0-1) for the MTM spectrum \code{Default=0.95}
#'@param demean_mtm Remove mean from data before conducting the MTM analysis \code{Default=TRUE}
#'@param detrend_mtm Remove mean from data before conducting the MTM analysis \code{Default=TRUE}
#'@param padfac_mtm Pad factor for the MTM analysis \code{Default=5}
#'@param tbw_mtm time bandwidth product of the MTM analysis \code{Default=3}
#'@param plot_horizontal plot the wavelet horizontal or vertical eg y axis is depth or y axis power \code{Default=TRUE}
#'
#'
#'
#' @return
#' The output is a plot of a cross wavelet scalogram.
#'
#' @author
#' 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.
#' \url{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.
#' \doi{10.1038/s41467-020-20539-9}
#'
#'@examples
#' \donttest{
#'#Example 1. A plot of a wavelet spectra using the Total Solar Irradiance
#'# data set of Steinhilber et al., (2012)
#'
#'TSI_wt <-
#' analyze_Awavelet(
#' data = TSI,
#' dj = 1/200,
#' lowerPeriod = 16,
#' upperPeriod = 8192,
#' verbose = FALSE,
#' omega_min = 6,
#' omega_max = 12,
#' scaling = "log2",
#' alpha = 1
#' )
#'
#'plot_Awavelet(
#' Awavelet = TSI_wt,
#' lowerPeriod = 16,
#' 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 = TRUE,
#' 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_wt <-
#'analyze_Awavelet(
#'data = mag,
#'dj = 1/100,
#'lowerPeriod = 1,
#'upperPeriod = 254,
#'verbose = FALSE,
#' omega_min = 6,
#' omega_max = 12,
#' scaling = "log2",
#' alpha = 1
#')
#'
#'plot_Awavelet(
#'Awavelet = mag_wt,
#'lowerPeriod = 1,
#'upperPeriod = 254,
#'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 = TRUE,
#'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_wt <-
#' analyze_Awavelet(
#' data = grey,
#' dj = 1/200,
#' lowerPeriod = 2,
#' upperPeriod = 25,
#' verbose = FALSE,
#' omega_min = 6,
#' omega_max = 12,
#' scaling = "log2",
#' alpha = 1)
#'
#'plot_Awavelet(
#'Awavelet = grey_wt,
#'lowerPeriod = 2,
#'upperPeriod = 25,
#'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 = TRUE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal=TRUE)
#'
#'}
#'
#'
#' @export
#' @importFrom stats quantile
#' @importFrom graphics par
#' @importFrom graphics image
#' @importFrom graphics axis
#' @importFrom graphics mtext
#' @importFrom graphics text
#' @importFrom graphics box
#' @importFrom graphics polygon
#' @importFrom graphics layout
#' @importFrom graphics title
#' @importFrom grDevices rgb
#' @importFrom DescTools Closest
#' @importFrom graphics abline
#' @importFrom RColorBrewer brewer.pal.info
#' @importFrom RColorBrewer brewer.pal
#' @importFrom grDevices colorRampPalette
#' @importFrom colorRamps blue2green
#' @importFrom colorRamps blue2green2red
#' @importFrom colorRamps blue2red
#' @importFrom colorRamps blue2yellow
#' @importFrom colorRamps cyan2yellow
#' @importFrom colorRamps green2red
#' @importFrom colorRamps magenta2green
#' @importFrom colorRamps matlab.like
#' @importFrom colorRamps matlab.like2
#' @importFrom colorRamps ygobb
#' @importFrom viridis viridis
#' @importFrom viridis magma
#' @importFrom viridis plasma
#' @importFrom viridis inferno
#' @importFrom viridis cividis
#' @importFrom viridis mako
#' @importFrom viridis rocket
#' @importFrom viridis turbo
#' @importFrom grDevices rainbow
#' @importFrom grDevices heat.colors
#' @importFrom grDevices terrain.colors
#' @importFrom grDevices topo.colors
#' @importFrom grDevices cm.colors
#' @importFrom grDevices hcl.colors
#' @importFrom RColorBrewer brewer.pal.info
#' @importFrom RColorBrewer brewer.pal
#' @importFrom grDevices colorRampPalette
#' @importFrom colorRamps blue2green
#' @importFrom colorRamps blue2green2red
#' @importFrom colorRamps blue2red
#' @importFrom colorRamps blue2yellow
#' @importFrom colorRamps cyan2yellow
#' @importFrom colorRamps green2red
#' @importFrom colorRamps magenta2green
#' @importFrom colorRamps matlab.like
#' @importFrom colorRamps matlab.like2
#' @importFrom colorRamps ygobb
#' @importFrom viridis viridis
#' @importFrom viridis magma
#' @importFrom viridis plasma
#' @importFrom viridis inferno
#' @importFrom viridis cividis
#' @importFrom viridis mako
#' @importFrom viridis rocket
#' @importFrom viridis turbo
#' @importFrom grDevices rainbow
#' @importFrom grDevices heat.colors
#' @importFrom grDevices terrain.colors
#' @importFrom grDevices topo.colors
#' @importFrom grDevices cm.colors
#' @importFrom grDevices hcl.colors
#' @importFrom scico scico
plot_Awavelet <- function(Awavelet = 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,
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) {
if (keep_editable == FALSE) {
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
}
maximum.level = max(Awavelet$Power)
power_max_mat.levels = quantile(Awavelet$Power, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
if (color_brewer== "RColorBrewer"){
key.cols <- rev(colorRampPalette(brewer.pal(brewer.pal.info[palette_name,1],palette_name))(n.levels))
}
if (color_brewer== "colorRamps"){
color_brewer_Sel <- paste("colorRamps::",palette_name,"(n=n.levels)")
key.cols = eval(parse(text = color_brewer_Sel))
}
if (color_brewer == "grDevices"){
if (palette_name == "rainbow"){
color_brewer_Sel <- "grDevices::rainbow(n=n.levels, start = 0, end = 0.7)"
key.cols <- rev(eval(parse(text = color_brewer_Sel)))
}
else if (palette_name == "heat.colors"|
palette_name == "terrain.colors"|
palette_name == "topo.colors"|
palette_name == "cm.colors"){
color_brewer_Sel <- paste("grDevices::",palette_name,"(n=n.levels, start = 0, end = 1)")
key.cols <- rev(eval(parse(text = color_brewer_Sel)))
}
else{
key.cols <- hcl.colors(n=n.levels, palette = palette_name, alpha = NULL, rev = FALSE, fixup = TRUE)}}
if (color_brewer== "scico"){
color_brewer_Sel <- paste(
"scico::scico(n = n.levels, palette = '",
palette_name,
"', direction = -1)",
sep = ""
)
key.cols = rev(eval(parse(text = color_brewer_Sel)))
}
if (color_brewer== "viridis"){
color_brewer_Sel <- paste("viridis::",palette_name,"(n=n.levels,direction = -1)")
key.cols = rev(eval(parse(text = color_brewer_Sel)))
}
periodtck = 0.02
periodtcl = 0.5
main = NULL
lwd = 2
lwd.axis = 1
legend.params = list(
width = 1.2,
shrink = 0.9,
mar = 5.1,
n.ticks = 6,
label.digits = 3,
label.format = "f",
lab = NULL,
lab.line = 2.5
)
key.marks = round(seq(from = 0, to = 1, length.out = legend.params$n.ticks) *
n.levels)
key.labels = formatC(as.numeric(power_max_mat.levels), digits = legend.params$label.digits,
format = legend.params$label.format)[key.marks + 1]
if(dev_new==TRUE & plot_horizontal==TRUE){
dev.new(width = 15,
height = 7,
noRStudioGD = TRUE)}
if(dev_new==TRUE & plot_horizontal==FALSE){
dev.new(width = 7,
height = 10,
noRStudioGD = TRUE)}
# y_axis <- as.numeric(unlist(Awavelet$Period))
pmax_avg_sel <- t(Awavelet$Power)
depth <- Awavelet$x
y_axis <- Awavelet$Period
depth <- as.numeric(depth)
y_axis <- as.numeric(y_axis)
MTM_res_2 <- matrix(data=NA,ncol=2,nrow=1)
if (add_MTM == TRUE | add_MTM_peaks == TRUE) {
MTM_res_1 <- mtm(
cbind(Awavelet$x, Awavelet$y),
tbw = tbw_mtm,
padfac = padfac_mtm,
output = 1,
siglevel = mtm_siglvl,
genplot = FALSE,
verbose = FALSE,
demean = demean_mtm,
detrend = detrend_mtm
)
MTM_res_2 <-
mtm(
cbind(Awavelet$x, Awavelet$y),
tbw = tbw_mtm,
padfac = padfac_mtm,
output = 3,
siglevel = mtm_siglvl,
genplot = FALSE,
verbose = FALSE,
demean = demean_mtm,
detrend = detrend_mtm
)
MTM_res_1$period <- 1 / MTM_res_1[, 1]
MTM_res_1$Peak <- 0
if (is.na(MTM_res_2[1,2]) == FALSE){
for (i in 1:nrow(MTM_res_2)) {
row_nr <- DescTools::Closest(MTM_res_1[, 1], MTM_res_2[i, 1], which = TRUE)
row_nr <- row_nr[1]
MTM_res_1[row_nr, 10] <- 1
}
}
mtm_res <- MTM_res_1
}
if (plot_dir != TRUE) {
xlim_vals = rev(c(min(Awavelet$x), max(Awavelet$x)))
} else{
xlim_vals = c(min(Awavelet$x), max(Awavelet$x))
}
if (is.null(lowerPeriod) == TRUE) {
lowerPeriod <- min(Awavelet$Period)
}
if (is.null(upperPeriod) == TRUE) {
upperPeriod <- max(Awavelet$Period)
}
ylim_vals = c(lowerPeriod, upperPeriod)
if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal==FALSE) {
layout.matrix <- matrix(c(1, 3, 0,2),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 0.25),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 4, 2, 0))
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(3, 0, 2, 2))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "")
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = "",
#axes = FALSE,
yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal==FALSE) {
layout.matrix <- matrix(c(1, 2),
nrow = 2,
ncol = 1 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 4),
# Heights of the two rows
widths = c(1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 4, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 2, 3))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(2,1,3,0,4,0,5,0),
nrow = 4,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,4),
# Heights of the two rows
widths = c(4, 1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 2, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 4, 0, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Ar. conf lvl",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Har. conf lvl",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(2,1,3,0,4,0,5,0,6,0),
nrow = 5,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,1,4),
# Heights of the two rows
widths = c(4, 1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 2, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 4, 0, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Ar. conf lvl",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Har. conf lvl",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xaxs = "i",
xlim = ylim_vals
)
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,0,3,0,4,0,5,6,7),
nrow = 5,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,1,4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 1, 2, 6),xpd=FALSE)
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = mean(key.marks), line = 4,
font = par()$font.axis, cex = par()$cex.axis,las=1)
box(lwd = lwd.axis)
par(mar = c(0,0, 2, 2),xpd=FALSE)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 0, 0, 2),xpd=FALSE)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
title(ylab="Ar. conf lvl",xpd=NA)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
title(ylab="Har. conf lvl",xpd=NA)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xaxs = "i",
xlim = ylim_vals
)
title(ylab="Wt. power",xpd=NA)
par( mar = c(4, 4, 0, 0),xpd=FALSE)
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
#ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
yaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,3,4),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 0.5, 2, 6),xpd=NA)
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(2, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 2, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = 1, line = 0.5,
font = par()$font.axis, cex = par()$cex.axis,las=1,xpd=NA)
#
box(lwd = lwd.axis)
par(mar = c(0,0, 2, 2))
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xlab="",
xaxs = "i",
xlim = ylim_vals
)
title(ylab="Wt. power",xpd=NA)
par(mar = c(4, 4, 0, 0),xpd=TRUE)
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
par(new = FALSE, mar = c(4, 0, 0, 2),xpd=FALSE)
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = "",
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
yaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,0,3,0,4,5,6),
nrow = 4,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 1, 2, 6),xpd=NA)
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = mean(key.marks), line = 4,
font = par()$font.axis, cex = par()$cex.axis,las=1)
box(lwd = lwd.axis)
par(mar = c(0,0, 2, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 0, 0, 2),xpd=FALSE)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
title(ylab="Ar. conf lvl",xpd=NA)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
title(ylab="Har. conf lvl",xpd=NA)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par( mar = c(4, 4, 0, 0))
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
#ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
yaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,0,3),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1,4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 2, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = median(key.marks), line = 3,
las = 2, font = par()$font.axis, cex = par()$cex.axis,xpd=NA)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xaxs = "i",
xlim = ylim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = (add_abline_v))
}
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal==TRUE) {
layout.matrix <- matrix(
c(1, 1, 1, 1, 1, 1, 2, 2, 2,
3, 3, 3, 3, 3, 3, 4, 5, 6),
nrow = 2,
ncol = 9 ,
byrow = TRUE
)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0 ,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 0))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE,mar = c(3, 2, 2, 2),
mgp = c(2, 1, 0))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "Power",
ylab = ""
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2)
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex=0.75)
box(lwd = lwd.axis)
par(new = FALSE,
mar = c(4, 4, 0, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
#
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal==TRUE) {
layout.matrix <- matrix(c(1, 2, 4, 3),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(8, 2))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 0))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE,
mar = c(3, 2, 2, 2),
mgp = c(2, 1, 0))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "Power",
ylab = ""
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2 )
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex=0.75)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(4, 4, 0, 0),xpd=FALSE)
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal ==TRUE ) {
layout.matrix <- matrix(c(1, 0, 3, 2),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(8, 2))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 2))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==TRUE) {
layout.matrix <- matrix(
c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2,
3, 3, 3, 3, 3, 3, 4, 5, 6, 7),
nrow = 2,
ncol = 10 ,
byrow = TRUE
)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 0))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE,
mar = c(3, 2, 2, 2),
mgp = c(2, 1, 0))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "Power",
ylab = ""
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2 )
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex=0.75)
box(lwd = lwd.axis)
par(new = FALSE,
mar = c(4, 4, 0, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal ==TRUE) {
layout.matrix <- matrix(c(3, 2, 1),
nrow = 1,
ncol = 3 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(6, 1, 1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE,
mar = c(4, 4, 2, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==TRUE) {
layout.matrix <-
matrix(c(6, 5, 4, 3, 2, 1),
nrow = 1,
ncol = 6 ,
byrow = TRUE)
graphics::layout(
mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(6, 1, 1, 1, 1, 1)
)
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col =key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = c(min(y_axis), max(y_axis)),
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE,
mar = c(4, 4, 2, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal==TRUE) {
layout.matrix <-
matrix(c(5, 4, 3, 2, 1),
nrow = 1,
ncol = 5 ,
byrow = TRUE)
graphics::layout(
mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(7, 1, 1, 1, 1)
)
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(new = FALSE,
mar = c(4, 4, 2, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal==TRUE) {
layout.matrix <- matrix(c(2, 1),
nrow = 1,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(10, 2.25))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 2, 0.5))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
return(invisible(mtm_res))
}
}
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Defines functions plot_Awavelet
Documented in plot_Awavelet
#' @title Plots a adaptive wavelet scalogram
#'
#' @description Plot adaptive wavelet scalogram using the outcome of the \code{\link{analyze_Awavelet}} function.
#'
#'@param Awavelet wavelet object created using the \code{\link{analyze_Awavelet}} function.
#'@param lowerPeriod Lowest period value which will be plotted
#'@param upperPeriod Highest period value which will be plotted
#'@param n.levels Number of color levels \code{Default=100}.
#'@param 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 \code{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”
#'@param 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. "\code{Default=grDevices}
#'@param useRaster Plot as a raster or vector image \code{Default=TRUE}.
#'WARNING plotting as a vector image is computationally intensive.
#'@param periodlab Label for the y-axis \code{Default="Period (metres)"}.
#'@param x_lab Label for the x-axis \code{Default="depth (metres)"}.
#'@param keep_editable Keep option to add extra features after plotting \code{Default=FALSE}
#'@param 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 \code{Default=TRUE}
#'@param 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 \code{plot_dir=TRUE}
#'@param 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 \code{Default=NULL}
#'@param 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 \code{Default=NULL}
#'@param add_abline_h Add horizontal lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) \code{Default=NULL}
#'@param add_abline_v Add vertical lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) \code{Default=NULL}
#'@param add_MTM_peaks Add the MTM peak periods as horizontal lines \code{Default=FALSE}
#'@param add_data Plot the data on top of the wavelet \code{Default=TRUE}
#'@param add_avg Plot the average wavelet spectral power to the side of the wavelet \code{Default=FALSE}
#'@param add_MTM Add the MTM plot next to the wavelet plot \code{Default=FALSE}
#'@param mtm_siglvl select the significance level (0-1) for the MTM spectrum \code{Default=0.95}
#'@param demean_mtm Remove mean from data before conducting the MTM analysis \code{Default=TRUE}
#'@param detrend_mtm Remove mean from data before conducting the MTM analysis \code{Default=TRUE}
#'@param padfac_mtm Pad factor for the MTM analysis \code{Default=5}
#'@param tbw_mtm time bandwidth product of the MTM analysis \code{Default=3}
#'@param plot_horizontal plot the wavelet horizontal or vertical eg y axis is depth or y axis power \code{Default=TRUE}
#'
#'
#'
#' @return
#' The output is a plot of a cross wavelet scalogram.
#'
#' @author
#' 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.
#' \url{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.
#' \doi{10.1038/s41467-020-20539-9}
#'
#'@examples
#' \donttest{
#'#Example 1. A plot of a wavelet spectra using the Total Solar Irradiance
#'# data set of Steinhilber et al., (2012)
#'
#'TSI_wt <-
#' analyze_Awavelet(
#' data = TSI,
#' dj = 1/200,
#' lowerPeriod = 16,
#' upperPeriod = 8192,
#' verbose = FALSE,
#' omega_min = 6,
#' omega_max = 12,
#' scaling = "log2",
#' alpha = 1
#' )
#'
#'plot_Awavelet(
#' Awavelet = TSI_wt,
#' lowerPeriod = 16,
#' 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 = TRUE,
#' 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_wt <-
#'analyze_Awavelet(
#'data = mag,
#'dj = 1/100,
#'lowerPeriod = 1,
#'upperPeriod = 254,
#'verbose = FALSE,
#' omega_min = 6,
#' omega_max = 12,
#' scaling = "log2",
#' alpha = 1
#')
#'
#'plot_Awavelet(
#'Awavelet = mag_wt,
#'lowerPeriod = 1,
#'upperPeriod = 254,
#'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 = TRUE,
#'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_wt <-
#' analyze_Awavelet(
#' data = grey,
#' dj = 1/200,
#' lowerPeriod = 2,
#' upperPeriod = 25,
#' verbose = FALSE,
#' omega_min = 6,
#' omega_max = 12,
#' scaling = "log2",
#' alpha = 1)
#'
#'plot_Awavelet(
#'Awavelet = grey_wt,
#'lowerPeriod = 2,
#'upperPeriod = 25,
#'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 = TRUE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal=TRUE)
#'
#'}
#'
#'
#' @export
#' @importFrom stats quantile
#' @importFrom graphics par
#' @importFrom graphics image
#' @importFrom graphics axis
#' @importFrom graphics mtext
#' @importFrom graphics text
#' @importFrom graphics box
#' @importFrom graphics polygon
#' @importFrom graphics layout
#' @importFrom graphics title
#' @importFrom grDevices rgb
#' @importFrom DescTools Closest
#' @importFrom graphics abline
#' @importFrom RColorBrewer brewer.pal.info
#' @importFrom RColorBrewer brewer.pal
#' @importFrom grDevices colorRampPalette
#' @importFrom colorRamps blue2green
#' @importFrom colorRamps blue2green2red
#' @importFrom colorRamps blue2red
#' @importFrom colorRamps blue2yellow
#' @importFrom colorRamps cyan2yellow
#' @importFrom colorRamps green2red
#' @importFrom colorRamps magenta2green
#' @importFrom colorRamps matlab.like
#' @importFrom colorRamps matlab.like2
#' @importFrom colorRamps ygobb
#' @importFrom viridis viridis
#' @importFrom viridis magma
#' @importFrom viridis plasma
#' @importFrom viridis inferno
#' @importFrom viridis cividis
#' @importFrom viridis mako
#' @importFrom viridis rocket
#' @importFrom viridis turbo
#' @importFrom grDevices rainbow
#' @importFrom grDevices heat.colors
#' @importFrom grDevices terrain.colors
#' @importFrom grDevices topo.colors
#' @importFrom grDevices cm.colors
#' @importFrom grDevices hcl.colors
#' @importFrom RColorBrewer brewer.pal.info
#' @importFrom RColorBrewer brewer.pal
#' @importFrom grDevices colorRampPalette
#' @importFrom colorRamps blue2green
#' @importFrom colorRamps blue2green2red
#' @importFrom colorRamps blue2red
#' @importFrom colorRamps blue2yellow
#' @importFrom colorRamps cyan2yellow
#' @importFrom colorRamps green2red
#' @importFrom colorRamps magenta2green
#' @importFrom colorRamps matlab.like
#' @importFrom colorRamps matlab.like2
#' @importFrom colorRamps ygobb
#' @importFrom viridis viridis
#' @importFrom viridis magma
#' @importFrom viridis plasma
#' @importFrom viridis inferno
#' @importFrom viridis cividis
#' @importFrom viridis mako
#' @importFrom viridis rocket
#' @importFrom viridis turbo
#' @importFrom grDevices rainbow
#' @importFrom grDevices heat.colors
#' @importFrom grDevices terrain.colors
#' @importFrom grDevices topo.colors
#' @importFrom grDevices cm.colors
#' @importFrom grDevices hcl.colors
#' @importFrom scico scico
plot_Awavelet <- function(Awavelet = 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,
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) {
if (keep_editable == FALSE) {
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
}
maximum.level = max(Awavelet$Power)
power_max_mat.levels = quantile(Awavelet$Power, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
if (color_brewer== "RColorBrewer"){
key.cols <- rev(colorRampPalette(brewer.pal(brewer.pal.info[palette_name,1],palette_name))(n.levels))
}
if (color_brewer== "colorRamps"){
color_brewer_Sel <- paste("colorRamps::",palette_name,"(n=n.levels)")
key.cols = eval(parse(text = color_brewer_Sel))
}
if (color_brewer == "grDevices"){
if (palette_name == "rainbow"){
color_brewer_Sel <- "grDevices::rainbow(n=n.levels, start = 0, end = 0.7)"
key.cols <- rev(eval(parse(text = color_brewer_Sel)))
}
else if (palette_name == "heat.colors"|
palette_name == "terrain.colors"|
palette_name == "topo.colors"|
palette_name == "cm.colors"){
color_brewer_Sel <- paste("grDevices::",palette_name,"(n=n.levels, start = 0, end = 1)")
key.cols <- rev(eval(parse(text = color_brewer_Sel)))
}
else{
key.cols <- hcl.colors(n=n.levels, palette = palette_name, alpha = NULL, rev = FALSE, fixup = TRUE)}}
if (color_brewer== "scico"){
color_brewer_Sel <- paste(
"scico::scico(n = n.levels, palette = '",
palette_name,
"', direction = -1)",
sep = ""
)
key.cols = rev(eval(parse(text = color_brewer_Sel)))
}
if (color_brewer== "viridis"){
color_brewer_Sel <- paste("viridis::",palette_name,"(n=n.levels,direction = -1)")
key.cols = rev(eval(parse(text = color_brewer_Sel)))
}
periodtck = 0.02
periodtcl = 0.5
main = NULL
lwd = 2
lwd.axis = 1
legend.params = list(
width = 1.2,
shrink = 0.9,
mar = 5.1,
n.ticks = 6,
label.digits = 3,
label.format = "f",
lab = NULL,
lab.line = 2.5
)
key.marks = round(seq(from = 0, to = 1, length.out = legend.params$n.ticks) *
n.levels)
key.labels = formatC(as.numeric(power_max_mat.levels), digits = legend.params$label.digits,
format = legend.params$label.format)[key.marks + 1]
if(dev_new==TRUE & plot_horizontal==TRUE){
dev.new(width = 15,
height = 7,
noRStudioGD = TRUE)}
if(dev_new==TRUE & plot_horizontal==FALSE){
dev.new(width = 7,
height = 10,
noRStudioGD = TRUE)}
# y_axis <- as.numeric(unlist(Awavelet$Period))
pmax_avg_sel <- t(Awavelet$Power)
depth <- Awavelet$x
y_axis <- Awavelet$Period
depth <- as.numeric(depth)
y_axis <- as.numeric(y_axis)
MTM_res_2 <- matrix(data=NA,ncol=2,nrow=1)
if (add_MTM == TRUE | add_MTM_peaks == TRUE) {
MTM_res_1 <- mtm(
cbind(Awavelet$x, Awavelet$y),
tbw = tbw_mtm,
padfac = padfac_mtm,
output = 1,
siglevel = mtm_siglvl,
genplot = FALSE,
verbose = FALSE,
demean = demean_mtm,
detrend = detrend_mtm
)
MTM_res_2 <-
mtm(
cbind(Awavelet$x, Awavelet$y),
tbw = tbw_mtm,
padfac = padfac_mtm,
output = 3,
siglevel = mtm_siglvl,
genplot = FALSE,
verbose = FALSE,
demean = demean_mtm,
detrend = detrend_mtm
)
MTM_res_1$period <- 1 / MTM_res_1[, 1]
MTM_res_1$Peak <- 0
if (is.na(MTM_res_2[1,2]) == FALSE){
for (i in 1:nrow(MTM_res_2)) {
row_nr <- DescTools::Closest(MTM_res_1[, 1], MTM_res_2[i, 1], which = TRUE)
row_nr <- row_nr[1]
MTM_res_1[row_nr, 10] <- 1
}
}
mtm_res <- MTM_res_1
}
if (plot_dir != TRUE) {
xlim_vals = rev(c(min(Awavelet$x), max(Awavelet$x)))
} else{
xlim_vals = c(min(Awavelet$x), max(Awavelet$x))
}
if (is.null(lowerPeriod) == TRUE) {
lowerPeriod <- min(Awavelet$Period)
}
if (is.null(upperPeriod) == TRUE) {
upperPeriod <- max(Awavelet$Period)
}
ylim_vals = c(lowerPeriod, upperPeriod)
if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal==FALSE) {
layout.matrix <- matrix(c(1, 3, 0,2),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 0.25),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 4, 2, 0))
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(3, 0, 2, 2))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "")
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = "",
#axes = FALSE,
yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal==FALSE) {
layout.matrix <- matrix(c(1, 2),
nrow = 2,
ncol = 1 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 4),
# Heights of the two rows
widths = c(1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 4, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 2, 3))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(2,1,3,0,4,0,5,0),
nrow = 4,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,4),
# Heights of the two rows
widths = c(4, 1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 2, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 4, 0, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Ar. conf lvl",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Har. conf lvl",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(2,1,3,0,4,0,5,0,6,0),
nrow = 5,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,1,4),
# Heights of the two rows
widths = c(4, 1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 2, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 2, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 4, 0, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Ar. conf lvl",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Har. conf lvl",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xaxs = "i",
xlim = ylim_vals
)
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
#
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,0,3,0,4,0,5,6,7),
nrow = 5,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,1,4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 1, 2, 6),xpd=FALSE)
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = mean(key.marks), line = 4,
font = par()$font.axis, cex = par()$cex.axis,las=1)
box(lwd = lwd.axis)
par(mar = c(0,0, 2, 2),xpd=FALSE)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 0, 0, 2),xpd=FALSE)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
title(ylab="Ar. conf lvl",xpd=NA)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
title(ylab="Har. conf lvl",xpd=NA)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xaxs = "i",
xlim = ylim_vals
)
title(ylab="Wt. power",xpd=NA)
par( mar = c(4, 4, 0, 0),xpd=FALSE)
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
#ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
yaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,3,4),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 0.5, 2, 6),xpd=NA)
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(2, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 2, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = 1, line = 0.5,
font = par()$font.axis, cex = par()$cex.axis,las=1,xpd=NA)
#
box(lwd = lwd.axis)
par(mar = c(0,0, 2, 2))
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xlab="",
xaxs = "i",
xlim = ylim_vals
)
title(ylab="Wt. power",xpd=NA)
par(mar = c(4, 4, 0, 0),xpd=TRUE)
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
par(new = FALSE, mar = c(4, 0, 0, 2),xpd=FALSE)
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = "",
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
yaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,0,3,0,4,5,6),
nrow = 4,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1, 1,1,4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 1, 2, 6),xpd=NA)
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = mean(key.marks), line = 4,
font = par()$font.axis, cex = par()$cex.axis,las=1)
box(lwd = lwd.axis)
par(mar = c(0,0, 2, 2))
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 2],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "MTM power",
xlab = "",
log = "x",
xlim = ylim_vals
)
for (i in 5:8) {
lines(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, i],
xlim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(mar = c(0, 0, 0, 2),xpd=FALSE)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 4],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "x",
ylim = c(80, 101),
xaxs = "i",
xlim = ylim_vals
)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
title(ylab="Ar. conf lvl",xpd=NA)
plot(
x = 1 / MTM_res_1[, 1],
y = MTM_res_1[, 3],
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "",
xlab = "",
log = "xy",
ylim = c(80, 101),
yaxs = "i",
xlim = ylim_vals
)
title(ylab="Har. conf lvl",xpd=NA)
abline(
h = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par( mar = c(4, 4, 0, 0))
plot(
x = Awavelet$y,
y = Awavelet$x,
type = "l",
yaxs = "i",
xlab = "proxy value",
ylab = x_lab,
#yaxt = "n",
ylim = xlim_vals
)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
#ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
yaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal ==FALSE) {
layout.matrix <- matrix(c(1,2,0,3),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1,4),
# Heights of the two rows
widths = c(1, 4))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(2, 2, 2, 3))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = median(key.marks), line = 3,
las = 2, font = par()$font.axis, cex = par()$cex.axis,xpd=NA)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(
y = Awavelet$Power.avg,
x = Awavelet$Period,
log = "x",
type = "l",
xaxs = "i",
xaxt = "n",
ylab = "Wt. power",
xaxs = "i",
xlim = ylim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = (add_abline_v))
}
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
y = Awavelet$x,
x = Awavelet$axis.2,
z = (Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
xlab = periodlab,
ylab = x_lab,
#axes = FALSE,
#yaxt = "n" ,
xaxt = "n" ,
main = main,
ylim = xlim_vals,
xlim = log2(ylim_vals)
)
# polygon(
# y=Awavelet$coi.1 ,
# x=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
1,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
mtext(
period.tick.label,
side = 1,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(y=add_lines[, 1], x=log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(y=add_points[, 1], x=log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(v = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal==TRUE) {
layout.matrix <- matrix(
c(1, 1, 1, 1, 1, 1, 2, 2, 2,
3, 3, 3, 3, 3, 3, 4, 5, 6),
nrow = 2,
ncol = 9 ,
byrow = TRUE
)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0 ,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 0))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE,mar = c(3, 2, 2, 2),
mgp = c(2, 1, 0))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "Power",
ylab = ""
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2)
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex=0.75)
box(lwd = lwd.axis)
par(new = FALSE,
mar = c(4, 4, 0, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
#
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal==TRUE) {
layout.matrix <- matrix(c(1, 2, 4, 3),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(8, 2))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 0))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE,
mar = c(3, 2, 2, 2),
mgp = c(2, 1, 0))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "Power",
ylab = ""
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2 )
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex=0.75)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(4, 4, 0, 0),xpd=FALSE)
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal ==TRUE ) {
layout.matrix <- matrix(c(1, 0, 3, 2),
nrow = 2,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(8, 2))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 2))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 0, 2))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==TRUE) {
layout.matrix <- matrix(
c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2,
3, 3, 3, 3, 3, 3, 4, 5, 6, 7),
nrow = 2,
ncol = 10 ,
byrow = TRUE
)
graphics::layout(mat = layout.matrix,
heights = c(0.25, 1),
# Heights of the two rows
widths = c(1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(0, 4, 2, 0))
plot(
y = Awavelet$y,
x = Awavelet$x,
type = "l",
xaxs = "i",
xlab = "",
ylab = "proxy value",
xaxt = "n",
xlim = xlim_vals
)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE,
mar = c(3, 2, 2, 2),
mgp = c(2, 1, 0))
image(
x = seq(from = 0, to = n.levels),
y = 1,
z = t(matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "Power",
ylab = ""
)
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2 )
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex=0.75)
box(lwd = lwd.axis)
par(new = FALSE,
mar = c(4, 4, 0, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == FALSE & plot_horizontal ==TRUE) {
layout.matrix <- matrix(c(3, 2, 1),
nrow = 1,
ncol = 3 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(6, 1, 1))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE,
mar = c(4, 4, 2, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE & plot_horizontal ==TRUE) {
layout.matrix <-
matrix(c(6, 5, 4, 3, 2, 1),
nrow = 1,
ncol = 6 ,
byrow = TRUE)
graphics::layout(
mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(6, 1, 1, 1, 1, 1)
)
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col =key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = c(min(y_axis), max(y_axis)),
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
x = Awavelet$Power.avg,
y = Awavelet$Period,
log = "y",
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Wt. power",
xaxs = "i",
ylim = ylim_vals
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE,
mar = c(4, 4, 2, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE & plot_horizontal==TRUE) {
layout.matrix <-
matrix(c(5, 4, 3, 2, 1),
nrow = 1,
ncol = 5 ,
byrow = TRUE)
graphics::layout(
mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(7, 1, 1, 1, 1)
)
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 3],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Har. conf lvl",
ylab = "",
log = "xy",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 4],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "Ar. conf lvl",
ylab = "",
log = "y",
xlim = c(80, 101),
xaxs = "i",
ylim = ylim_vals
)
abline(
v = c(90, 95, 99),
lty = 3,
col = "grey",
lwd = 2
)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
plot(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, 2],
type = "l",
yaxs = "i",
yaxt = "n",
xlab = "MTM power",
ylab = "",
log = "y",
ylim = ylim_vals
)
for (i in 5:8) {
lines(
y = 1 / MTM_res_1[, 1],
x = MTM_res_1[, i],
ylim = ylim_vals,
lty = 3,
col = "grey",
lwd = 2
)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = 1 / MTM_res_2[, 1],
col = "red",
lty = 3)
}
par(new = FALSE,
mar = c(4, 4, 2, 0),
mgp = c(2, 1, 0))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE & plot_horizontal==TRUE) {
layout.matrix <- matrix(c(2, 1),
nrow = 1,
ncol = 2 ,
byrow = TRUE)
graphics::layout(mat = layout.matrix,
heights = c(1),
# Heights of the two rows
widths = c(10, 2.25))
power_max_mat.levels = quantile(pmax_avg_sel,
probs = seq(
from = 0,
to = 1,
length.out = n.levels + 1
))
par(mar = c(4, 0, 2, 5))
image(
y = seq(from = 0, to = n.levels),
x = 1,
z = (matrix(power_max_mat.levels,
nrow = 1)),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
yaxt = "n",
xaxt = "n",
xlab = "",
ylab = "",
)
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 4, at = mean(key.marks), line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 2, 0.5))
image(
x = Awavelet$x,
y = Awavelet$axis.2,
z = t(Awavelet$Power),
col = key.cols,
breaks = power_max_mat.levels,
useRaster = TRUE,
ylab = periodlab,
xlab = x_lab,
axes = TRUE,
yaxt = "n" ,
main = main,
xlim = xlim_vals,
ylim = log2(ylim_vals)
)
# polygon(
# x=Awavelet$coi.1 ,
# y=Awavelet$coi.2,
# border = NA,
# col = rgb(1, 1, 1, 0.5),
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
box(lwd = lwd.axis)
period.tick = unique(trunc(Awavelet$axis.2))
period.tick[period.tick < log2(Awavelet$Period[1])] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2 ^ (period.tick)
axis(
2,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
axis(
4,
lwd = lwd.axis,
at = period.tick,
labels = NA,
tck = periodtck,
tcl = periodtcl
)
mtext(
period.tick.label,
side = 2,
at = period.tick,
las = 2,
line = par()$mgp[2] - 0.5,
font = par()$font.axis,
cex = par()$cex.axis
)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines))
lines(add_lines[, 1], log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points))
points(add_points[, 1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
abline(h = log2(1 / MTM_res_2[, 1]),
col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1,2]) == FALSE) {
return(invisible(mtm_res))
}
}
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