Nothing
R/plot_eha_log2.R
In WaverideR: Extracting Signals from Wavelet Spectra
#' @title Plots an log2 spaced EHA spectra
#'
#' @description Plot wavelet scalogram using the outcome of the \code{\link{eha_log2}} function.
#'
#'@param eha_log2 eha_log2 object created using the \code{\link{eha_log2}} function.
#'@param plot_opt plot options are "Power", "Amplitude", "Probability" or "F_test"
#'@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}
#'@param pval_abline p value of the abline
#'@param pval_cutoff p value cutoff below which no data is displayed
#'
#' @return
#' The output is a plot of a EHA spectra.
#' if add_MTM_peaks = TRUE then the output of the MTM analysis will given as matrix
#'
#' @author
#' Code based on the wt.image" functions of the 'WaveletComp' R package
#' The EHA and MTM analysis parts are from the astrochron R package of Meyers et al., (2012)
#'
#' @references
#'Angi Roesch and Harald Schmidbauer (2018). WaveletComp: Computational
#'Wavelet Analysis. R package version 1.1.
#'\url{https://CRAN.R-project.org/package=WaveletComp}
#'
#'S.R. Meyers, 2012, Seeing Red in Cyclic Stratigraphy: Spectral Noise Estimation for
#'Astrochronology: Paleoceanography, 27, PA3228, <doi:10.1029/2012PA002307>
#'
#'S.R. Meyers, 2019 Cyclostratigraphy and the problem of astrochronologic testing, Earth-Science Reviews,
#'Volume 190, <doi.org/10.1016/j.earscirev.2018.11.015.>
#'
#'@examples
#' \donttest{
#'#Example 1. A plot of a wavelet spectra using the Total Solar Irradiance
#'# data set of Steinhilber et al., (2012)
#'
#'TSI_eha_log2 <- eha_log2(data = TSI,
#'win = 8192,
#'tbw = 4,
#'demean = TRUE,
#'detrend = TRUE,
#'upperPeriod = 8192,
#'lowerPeriod = 50,
#'pad = NULL,
#'padding = "noise")
#'
#'plot_eha_log2(
#'eha_log2 = TSI_eha_log2,
#'plot_opt = "Amplitude",
#'lowerPeriod = 50,
#'upperPeriod = 8192,
#'n.levels = 100,
#'palette_name = "rainbow",
#'color_brewer = "grDevices",
#'useRaster = TRUE,
#'periodlab = "Period (metres)",
#'x_lab = "depth (metres)",
#'keep_editable = FALSE,
#'dev_new = TRUE,
#'plot_dir = TRUE,
#'add_lines = NULL,
#'add_points = NULL,
#'add_abline_h = NULL,
#'add_abline_v = NULL,
#'add_MTM_peaks = FALSE,
#'add_data = TRUE,
#'add_avg = FALSE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal = TRUE)
#'
#'#Example 2. A plot of a wavelet spectra using the magnetic susceptibility
#'#data set of Pas et al., (2018)
#'mag_eha_log2 <- eha_log2(data = mag,
#'win = 50,
#'tbw = 4,
#'demean = TRUE,
#'detrend = TRUE,
#'upperPeriod = 50,
#'lowerPeriod = 1,
#'pad = NULL,
#'padding = "noise")
#'
#'plot_eha_log2(
#'eha_log2 = mag_eha_log2,
#'plot_opt = "Amplitude",
#'lowerPeriod = 1,
#'upperPeriod = 50,
#'n.levels = 100,
#'palette_name = "rainbow",
#'color_brewer = "grDevices",
#'useRaster = TRUE,
#'periodlab = "Period (metres)",
#'x_lab = "depth (metres)",
#'keep_editable = FALSE,
#'dev_new = TRUE,
#'plot_dir = TRUE,
#'add_lines = NULL,
#'add_points = NULL,
#'add_abline_h = NULL,
#'add_abline_v = NULL,
#'add_MTM_peaks = FALSE,
#'add_data = TRUE,
#'add_avg = FALSE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal = TRUE)
#'
#'
#'#Example 3. A plot of a wavelet spectra using the greyscale
#'# data set of Zeeden et al., (2013)
#'grey_eha_log2 <- eha_log2(data = grey,
#'win = 20,
#'tbw = 4,
#'demean = TRUE,
#'detrend = TRUE,
#'upperPeriod = 20,
#'lowerPeriod = 1,
#'pad = NULL,
#'padding = "noise")
#'
#'
#'plot_eha_log2(
#'eha_log2 = grey_eha_log2,
#'plot_opt = "Amplitude",
#'lowerPeriod = 1,
#'upperPeriod = 20,
#'n.levels = 100,
#'palette_name = "rainbow",
#'color_brewer = "grDevices",
#'useRaster = TRUE,
#'periodlab = "Period (metres)",
#'x_lab = "depth (metres)",
#'keep_editable = FALSE,
#'dev_new = TRUE,
#'plot_dir = TRUE,
#'add_lines = NULL,
#'add_points = NULL,
#'add_abline_h = NULL,
#'add_abline_v = NULL,
#'add_MTM_peaks = FALSE,
#'add_data = TRUE,
#'add_avg = FALSE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal = TRUE)
#'}
#'
#' @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 astrochron mtm
#' @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_eha_log2 <- function (eha_log2 = NULL, plot_opt = "Amplitude", lowerPeriod = NULL,
upperPeriod = NULL, n.levels = 100, palette_name = "rainbow",
color_brewer = "grDevices", useRaster = TRUE, periodlab = "Period (metres)",
x_lab = "depth (metres)", keep_editable = FALSE, dev_new = TRUE,
plot_dir = TRUE, add_lines = NULL, add_points = NULL, add_abline_h = NULL,
add_abline_v = NULL, add_MTM_peaks = FALSE, add_data = TRUE,
add_avg = FALSE, pval_abline = c(0.1, 0.05), pval_cutoff = c(0.1),
add_MTM = FALSE, mtm_siglvl = 0.95, demean_mtm = TRUE, detrend_mtm = TRUE,
padfac_mtm = 5, tbw_mtm = 3, plot_horizontal = TRUE)
{
if (plot_opt == "Amplitude") {
mat <- eha_log2$amp
average <- eha_log2$amp.avg
}
else if (plot_opt == "Power") {
mat <- eha_log2$pwr
average <- eha_log2$pwr.avg
}
else if (plot_opt == "Probability") {
mat <- eha_log2$prob
average <- eha_log2$prob.avg
}
else if (plot_opt == "F_test") {
mat <- eha_log2$f_test
average <- eha_log2$f_test.avg
}
else {
mat <- eha_log2$amp
average <- eha_log2$amp.avg
}
if (keep_editable == FALSE) {
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
}
maximum.level = max(mat, na.rm = TRUE)
power_max_mat.levels = quantile(mat, na.rm = TRUE, 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$label.format)[key.marks + 1]
if (dev_new == TRUE & plot_horizontal == TRUE) {
dev.new(width = 15, height = 7, noRStudioGD = TRUE)
}
if (dev_new == TRUE & plot_horizontal == FALSE) {
dev.new(width = 7, height = 10, noRStudioGD = TRUE)
}
depth <- eha_log2$depth
y_axis <- eha_log2$log2_period
depth <- as.numeric(depth)
y_axis <- as.numeric(y_axis)
MTM_res_2 <- matrix(data = NA, ncol = 2, nrow = 1)
if (add_MTM == TRUE | add_MTM_peaks == TRUE) {
MTM_res_1 <- mtm(cbind(eha_log2$x, eha_log2$y), tbw = tbw_mtm,
padfac = padfac_mtm, output = 1, siglevel = mtm_siglvl,
genplot = FALSE, verbose = FALSE, demean = demean_mtm,
detrend = detrend_mtm)
MTM_res_2 <- mtm(cbind(eha_log2$x, eha_log2$y), tbw = tbw_mtm,
padfac = padfac_mtm, output = 3, siglevel = mtm_siglvl,
genplot = FALSE, verbose = FALSE, demean = demean_mtm,
detrend = detrend_mtm)
MTM_res_1$period <- 1/MTM_res_1[, 1]
MTM_res_1$Peak <- 0
if (is.na(MTM_res_2[1, 2]) == FALSE) {
for (i in 1:nrow(MTM_res_2)) {
row_nr <- DescTools::Closest(MTM_res_1[, 1],
MTM_res_2[i, 1], which = TRUE)
row_nr <- row_nr[1]
MTM_res_1[row_nr, 10] <- 1
}
}
mtm_res <- MTM_res_1
}
if (plot_dir != TRUE) {
xlim_vals = rev(c(min(eha_log2$x), max(eha_log2$x)))
}
else {
xlim_vals = c(min(eha_log2$x), max(eha_log2$x))
}
if (is.null(lowerPeriod) == TRUE) {
lowerPeriod <- min(eha_log2$Period)
}
if (is.null(upperPeriod) == TRUE) {
upperPeriod <- max(eha_log2$Period)
}
ylim_vals = c(lowerPeriod, upperPeriod)
if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(1, 3, 0, 2), nrow = 2, ncol = 2,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
0.25), widths = c(1, 4))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(4, 4, 2, 0))
plot(x = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(3, 0, 2, 2))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "")
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = "", yaxt = "n",
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
period.tick = unique(trunc( as.numeric(eha_log2$log2_period)))
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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(1, 2), nrow = 2, ncol = 1,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
4), widths = c(1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(2, 4, 2, 3))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 2, 3))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(2, 1, 3, 0, 4, 0, 5, 0), nrow = 4,
ncol = 2, byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
1, 1, 4), widths = c(4, 1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(2, 2, 2, 3))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 2], type = "l",
xaxs = "i", xaxt = "n", ylab = "MTM power", xlab = "",
log = "x", xlim = ylim_vals)
for (i in 5:8) {
lines(x = 1/MTM_res_1[, 1], y = MTM_res_1[, i],
xlim = ylim_vals, lty = 3, col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(mar = c(0, 4, 0, 2))
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 4], type = "l",
xaxs = "i", xaxt = "n", ylab = "Ar. conf lvl", xlab = "",
log = "x", ylim = c(80, 101), xaxs = "i", xlim = ylim_vals)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 3], type = "l",
xaxs = "i", xaxt = "n", ylab = "Har. conf lvl",
xlab = "", log = "xy", ylim = c(80, 101), yaxs = "i",
xlim = ylim_vals)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(new = FALSE, mar = c(4, 4, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(as.numeric(eha_log2$log2_period)))
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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(2, 1, 3, 0, 4, 0, 5, 0, 6,
0), nrow = 5, ncol = 2, byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
1, 1, 1, 4), widths = c(4, 1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(2, 2, 2, 3))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 2], type = "l",
xaxs = "i", xaxt = "n", ylab = "MTM power", xlab = "",
log = "x", xlim = ylim_vals)
for (i in 5:8) {
lines(x = 1/MTM_res_1[, 1], y = MTM_res_1[, i],
xlim = ylim_vals, lty = 3, col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(mar = c(0, 4, 0, 2))
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 4], type = "l",
xaxs = "i", xaxt = "n", ylab = "Ar. conf lvl", xlab = "",
log = "x", ylim = c(80, 101), xaxs = "i", xlim = ylim_vals)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 3], type = "l",
xaxs = "i", xaxt = "n", ylab = "Har. conf lvl",
xlab = "", log = "xy", ylim = c(80, 101), yaxs = "i",
xlim = ylim_vals)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = average, x = 2^eha_log2$log2_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 = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(1, 4))
power_max_mat.levels = quantile(mat, 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 = average, x = 2^eha_log2$log2_period, log = "x",
type = "l", xaxs = "i", xaxt = "n", ylab = "Wt. power",
xaxs = "i", xlim = ylim_vals)
title(ylab = "Wt. power", xpd = NA)
par(mar = c(4, 4, 0, 0), xpd = FALSE)
plot(x = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, xaxt = "n",
yaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(as.numeric(eha_log2$log2_period)))
period.tick[period.tick < log2(as.numeric(eha_log2$log2_period[1]))] = NA
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(1, 4))
power_max_mat.levels = quantile(mat, 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 = average, x = 2^eha_log2$log2_period, log = "x",
type = "l", xaxs = "i", xaxt = "n", ylab = "Wt. power",
xlab = "", xaxs = "i", xlim = ylim_vals)
title(ylab = "Wt. power", xpd = NA)
par(mar = c(4, 4, 0, 0), xpd = TRUE)
plot(x = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
par(new = FALSE, mar = c(4, 0, 0, 2), xpd = FALSE)
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = "", xaxt = "n",
yaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(1, 2, 0, 3, 0, 4, 5, 6), nrow = 4,
ncol = 2, byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
1, 1, 4), widths = c(1, 4))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 1, 2, 6), xpd = NA)
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = mean(key.marks), line = 4,
font = par()$font.axis, cex = par()$cex.axis, las = 1)
box(lwd = lwd.axis)
par(mar = c(0, 0, 2, 2))
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 2], type = "l",
xaxs = "i", xaxt = "n", ylab = "MTM power", xlab = "",
log = "x", xlim = ylim_vals)
for (i in 5:8) {
lines(x = 1/MTM_res_1[, 1], y = MTM_res_1[, i],
xlim = ylim_vals, lty = 3, col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(mar = c(0, 0, 0, 2), xpd = FALSE)
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 4], type = "l",
xaxs = "i", xaxt = "n", ylab = "", xlab = "", log = "x",
ylim = c(80, 101), xaxs = "i", xlim = ylim_vals)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
title(ylab = "Ar. conf lvl", xpd = NA)
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 3], type = "l",
xaxs = "i", xaxt = "n", ylab = "", xlab = "", log = "xy",
ylim = c(80, 101), yaxs = "i", xlim = ylim_vals)
title(ylab = "Har. conf lvl", xpd = NA)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(mar = c(4, 4, 0, 0))
plot(x = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, xaxt = "n",
yaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == FALSE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(1, 2, 0, 3), nrow = 2, ncol = 2,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
4), widths = c(1, 4))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(2, 2, 2, 3))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis,
xpd = NA)
box(lwd = lwd.axis)
par(mar = c(0, 4, 2, 2))
plot(y = average, x = 2^eha_log2$log2_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 = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 0))
plot(y = eha_log2$y, x = eha_log2$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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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), widths = c(8, 2))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 0))
plot(y = eha_log2$y, x = eha_log2$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 = average, y = 2^eha_log2$log2_period, log = "y",
type = "l", yaxs = "i", yaxt = "n", xlab = "Wt. power",
xaxs = "i", ylim = ylim_vals)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "black", lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(4, 4, 0, 0), xpd = FALSE)
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(1, 0, 3, 2), nrow = 2, ncol = 2,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(0.25,
1), widths = c(8, 2))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 2))
plot(y = eha_log2$y, x = eha_log2$x, type = "l", xaxs = "i",
xlab = "", ylab = "proxy value", xaxt = "n", xlim = xlim_vals)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 2, 5))
image(y = seq(from = 0, to = n.levels), x = 1, z = (matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 0, 2))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(1, 1, 1, 1, 1, 1, 2, 2, 2,
2, 3, 3, 3, 3, 3, 3, 4, 5, 6, 7), nrow = 2, ncol = 10,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(0.25,
1), widths = c(1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 0))
plot(y = eha_log2$y, x = eha_log2$x, type = "l", xaxs = "i",
xlab = "", ylab = "proxy value", xaxt = "n", xlim = xlim_vals)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(3, 2, 2, 2), mgp = c(2, 1,
0))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "Power",
ylab = "")
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2)
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex = 0.75)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 0, 0), mgp = c(2, 1,
0))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(x = average, y = 2^eha_log2$log2_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),
widths = c(6, 1, 1))
power_max_mat.levels = quantile(mat, 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 = average, y = 2^eha_log2$log2_period, log = "y",
type = "l", yaxs = "i", yaxt = "n", xlab = "Wt. power",
xaxs = "i", ylim = ylim_vals)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "black", lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(4, 4, 2, 0), mgp = c(2, 1,
0))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(6, 5, 4, 3, 2, 1), nrow = 1,
ncol = 6, byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1),
widths = c(6, 1, 1, 1, 1, 1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(4, 0, 2, 5))
image(y = seq(from = 0, to = n.levels), x = 1, z = (matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 3], type = "l",
yaxs = "i", yaxt = "n", xlab = "Har. conf lvl",
ylab = "", log = "xy", xlim = c(80, 101), xaxs = "i",
ylim = ylim_vals)
abline(v = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 4], type = "l",
yaxs = "i", yaxt = "n", xlab = "Ar. conf lvl", ylab = "",
log = "y", xlim = c(80, 101), xaxs = "i", ylim = ylim_vals)
abline(v = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 2], type = "l",
yaxs = "i", yaxt = "n", xlab = "MTM power", ylab = "",
log = "y", ylim = ylim_vals)
for (i in 5:8) {
lines(y = 1/MTM_res_1[, 1], x = MTM_res_1[, i],
ylim = c(min(y_axis), max(y_axis)), lty = 3,
col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(x = average, y = 2^eha_log2$log2_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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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),
widths = c(7, 1, 1, 1, 1))
power_max_mat.levels = quantile(mat, 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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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),
widths = c(10, 2.25))
power_max_mat.levels = quantile(mat, 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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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))
}
}
### old function keep for now #
#
# plot_eha_log2 <- function (eha_log2 = NULL,
# plot_opt = "Amplitude",
# lowerPeriod = NULL,
# upperPeriod = NULL,
# n.levels = 100,
# palette_name = "rainbow",
# color_brewer = "grDevices",
# useRaster = TRUE,
# periodlab = "Period (metres)",
# x_lab = "depth (metres)",
# keep_editable = FALSE,
# dev_new = TRUE,
# plot_dir = TRUE,
# add_lines = NULL,
# add_points = NULL,
# add_abline_h = NULL,
# add_abline_v = NULL,
# add_MTM_peaks = FALSE,
# add_data = TRUE,
# add_avg = FALSE,
# pval_abline = c(0.1, 0.05),
# pval_cutoff = c(0.1),
# add_MTM = FALSE,
# mtm_siglvl = 0.95,
# demean_mtm = TRUE,
# detrend_mtm = TRUE,
# padfac_mtm = 5,
# tbw_mtm = 3,
# plot_horizontal = TRUE)
# {
# if (plot_opt == "Amplitude") {
# mat <- eha_log2$amp
# average <- eha_log2$amp.avg} else if (plot_opt == "Power") {
# mat <- eha_log2$pwr
# average <- eha_log2$pwr.avg} else if (plot_opt == "Probability") {
# mat <- eha_log2$prob
# average <- eha_log2$prob.avg} else if (plot_opt == "F_test") {
# mat <- eha_log2$f_test
# average <- eha_log2$f_test.avg} else{
# mat <- eha_log2$amp
# average <- eha_log2$amp.avg
# }
#
#
# if (keep_editable == FALSE) {
# oldpar <- par(no.readonly = TRUE)
# on.exit(par(oldpar))
# }
# maximum.level = max(mat,na.rm=TRUE)
# power_max_mat.levels = quantile(mat,na.rm=TRUE, 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 == "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$label.format
# )[key.marks + 1]
# if (dev_new == TRUE & plot_horizontal == TRUE) {
# dev.new(width = 15,
# height = 7,
# noRStudioGD = TRUE)
# }
# if (dev_new == TRUE & plot_horizontal == FALSE) {
# dev.new(width = 7,
# height = 10,
# noRStudioGD = TRUE)
# }
#
# depth <- eha_log2$depth
# y_axis <- eha_log2$log2_period
# depth <- as.numeric(depth)
# y_axis <- as.numeric(y_axis)
# MTM_res_2 <- matrix(data = NA,
# ncol = 2,
# nrow = 1)
# if (add_MTM == TRUE | add_MTM_peaks == TRUE) {
# MTM_res_1 <- mtm(
# cbind(eha_log2$x, eha_log2$y),
# tbw = tbw_mtm,
# padfac = padfac_mtm,
# output = 1,
# siglevel = mtm_siglvl,
# genplot = FALSE,
# verbose = FALSE,
# demean = demean_mtm,
# detrend = detrend_mtm
# )
# MTM_res_2 <- mtm(
# cbind(eha_log2$x, eha_log2$y),
# tbw = tbw_mtm,
# padfac = padfac_mtm,
# output = 3,
# siglevel = mtm_siglvl,
# genplot = FALSE,
# verbose = FALSE,
# demean = demean_mtm,
# detrend = detrend_mtm
# )
# MTM_res_1$period <- 1 / MTM_res_1[, 1]
# MTM_res_1$Peak <- 0
# if (is.na(MTM_res_2[1, 2]) == FALSE) {
# for (i in 1:nrow(MTM_res_2)) {
# row_nr <- DescTools::Closest(MTM_res_1[, 1], MTM_res_2[i, 1], which = TRUE)
# row_nr <- row_nr[1]
# MTM_res_1[row_nr, 10] <- 1
# }
# }
# mtm_res <- MTM_res_1
# }
# if (plot_dir != TRUE) {
# xlim_vals = rev(c(min(eha_log2$x), max(eha_log2$x)))
# }else {
# xlim_vals = c(min(eha_log2$x), max(eha_log2$x))
# }
# if (is.null(lowerPeriod) == TRUE) {
# lowerPeriod <- min(eha_log2$Period)
# }
# if (is.null(upperPeriod) == TRUE) {
# upperPeriod <- max(eha_log2$Period)
# }
#
#
# ylim_vals = c(lowerPeriod, upperPeriod)
# if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(c(1, 3, 0, 2),
# nrow = 2,
# ncol = 2,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1, 0.25),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(4, 4, 2, 0))
# plot(
# x = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# if (is.null(add_abline_h) != TRUE) {
# abline(h = add_abline_h)
# }
# par(new = FALSE, mar = c(3, 0, 2, 2))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = ""
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 0, 2, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = "",
# yaxt = "n",
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# period.tick = unique(trunc(eha_log2$log2_period))
# #period.tick[period.tick < log2(eha_log2$Period[1])] = NA
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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) {
# #graphics.off()
# layout.matrix <- matrix(c(1, 2),
# nrow = 2,
# ncol = 1,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1, 4),
# widths = c(1))
# power_max_mat.levels = quantile(mat, 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 = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# }
# 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),
# widths = c(4, 1))
# power_max_mat.levels = quantile(mat, 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 = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(4, 1)
# )
# power_max_mat.levels = quantile(mat, 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 = average,
# x = 2^eha_log2$log2_period,
# log = "x",
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Wt. power",
# xaxs = "i",
# xlim = ylim_vals
# )
# par(new = FALSE, mar = c(4, 4, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
#
# if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(
# c(1, 2, 0, 3, 0, 4, 0, 5, 6, 7),
# nrow = 5,
# ncol = 2,
# byrow = TRUE
# )
# graphics::layout(
# mat = layout.matrix,
# heights = c(1, 1, 1, 1, 4),
# widths = c(1, 4)
# )
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 1, 2, 6), xpd = FALSE)
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# mtext(
# c("Power"),
# side = 1,
# at = mean(key.marks),
# line = 4,
# font = par()$font.axis,
# cex = par()$cex.axis,
# las = 1
# )
# box(lwd = lwd.axis)
# par(mar = c(0, 0, 2, 2), xpd = FALSE)
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 2],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "MTM power",
# xlab = "",
# log = "x",
# xlim = ylim_vals
# )
# for (i in 5:8) {
# lines(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, i],
# xlim = ylim_vals,
# lty = 3,
# col = "grey",
# lwd = 2
# )
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(mar = c(0, 0, 0, 2), xpd = FALSE)
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 4],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "",
# xlab = "",
# log = "x",
# ylim = c(80, 101),
# xaxs = "i",
# xlim = ylim_vals
# )
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# title(ylab = "Ar. conf lvl", xpd = NA)
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 3],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "",
# xlab = "",
# log = "xy",
# ylim = c(80, 101),
# yaxs = "i",
# xlim = ylim_vals
# )
# title(ylab = "Har. conf lvl", xpd = NA)
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# y = average,
# x = 2^eha_log2$log2_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 = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# par(new = FALSE, mar = c(4, 0, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# xaxt = "n",
# yaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$axis.2))
# period.tick[period.tick < log2(eha_log2$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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
# if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(c(1, 2, 3, 4),
# nrow = 2,
# ncol = 2,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1, 4),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(2, 0.5, 2, 6), xpd = NA)
# image(
# y = seq(from = 0, to = n.levels),
# x = 1,
# z = (matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 2,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 2,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# mtext(
# c("Power"),
# side = 1,
# at = 1,
# line = 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis,
# las = 1,
# xpd = NA
# )
# box(lwd = lwd.axis)
# par(mar = c(0, 0, 2, 2))
# plot(
# y = average,
# x = 2^eha_log2$log2_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 = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# par(new = FALSE,
# mar = c(4, 0, 0, 2),
# xpd = FALSE)
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = "",
# xaxt = "n",
# yaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, 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 = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# par(new = FALSE, mar = c(4, 0, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# xaxt = "n",
# yaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, 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 = average,
# x = 2^eha_log2$log2_period,
# log = "x",
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Wt. power",
# xaxs = "i",
# xlim = ylim_vals
# )
# if (is.null(add_abline_v) != TRUE) {
# abline(v = (add_abline_v))
# }
# par(new = FALSE, mar = c(4, 4, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
#
#
#
#
# if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE &
# plot_horizontal == TRUE) {
# layout.matrix <- matrix(
# c(1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 5, 6),
# nrow = 2,
# ncol = 9,
# byrow = TRUE
# )
# graphics::layout(mat = layout.matrix,
# heights = c(0.25, 1),
# widths = c(1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 0))
# plot(
# y = eha_log2$y,
# x = eha_log2$x,
# type = "l",
# xaxs = "i",
# xlab = "",
# ylab = "proxy value",
# xaxt = "n",
# xlim = xlim_vals
# )
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# par(new = FALSE,
# mar = c(3, 2, 2, 2),
# mgp = c(2, 1, 0))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "Power",
# ylab = ""
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.2
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.1,
# las = 2,
# cex = 0.75
# )
# box(lwd = lwd.axis)
# par(new = FALSE,
# mar = c(4, 4, 0, 0),
# mgp = c(2, 1, 0))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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),
# widths = c(8, 2))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 0))
# plot(
# y = eha_log2$y,
# x = eha_log2$x,
# type = "l",
# xaxs = "i",
# xlab = "",
# ylab = "proxy value",
# xaxt = "n",
# xlim = xlim_vals
# )
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# par(new = FALSE,
# mar = c(3, 2, 2, 2),
# mgp = c(2, 1, 0))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "Power",
# ylab = ""
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.2
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.1,
# las = 2,
# cex = 0.75
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 0, 0, 0.5))
# plot(
# x = average,
# y = 2^eha_log2$log2_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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(8, 2))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 2))
# plot(
# y = eha_log2$y,
# x = eha_log2$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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 0))
# plot(
# y = eha_log2$y,
# x = eha_log2$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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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 = average,
# y = 2^eha_log2$log2_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),
# widths = c(6, 1, 1))
# power_max_mat.levels = quantile(mat, 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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 0, 2, 0.5))
# plot(
# x = average,
# y = 2^eha_log2$log2_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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(6, 1, 1, 1, 1, 1)
# )
# power_max_mat.levels = quantile(mat, 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 = average,
# y = 2^eha_log2$log2_period,
# log = "y",
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Wt. power",
# xaxs = "i",
# ylim = ylim_vals
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = add_abline_h)
# }
# par(new = FALSE,
# mar = c(4, 4, 2, 0),
# mgp = c(2, 1, 0))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(add_lines[, 1], log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(add_points[, 1], log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = log2(add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# }
# if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE &
# plot_horizontal == TRUE) {
# layout.matrix <- matrix(c(5, 4, 3, 2, 1),
# nrow = 1,
# ncol = 5,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1),
# widths = c(7, 1, 1, 1, 1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(4, 0, 2, 5))
# image(
# y = seq(from = 0, to = n.levels),
# x = 1,
# z = (matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 4,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 0, 2, 0.5))
# plot(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, 3],
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Har. conf lvl",
# ylab = "",
# log = "xy",
# xlim = c(80, 101),
# xaxs = "i",
# ylim = ylim_vals
# )
# abline(
# v = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, 4],
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Ar. conf lvl",
# ylab = "",
# log = "y",
# xlim = c(80, 101),
# xaxs = "i",
# ylim = ylim_vals
# )
# abline(
# v = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, 2],
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "MTM power",
# ylab = "",
# log = "y",
# ylim = ylim_vals
# )
# for (i in 5:8) {
# lines(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, i],
# ylim = ylim_vals,
# lty = 3,
# col = "grey",
# lwd = 2
# )
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(new = FALSE,
# mar = c(4, 4, 2, 0),
# mgp = c(2, 1, 0))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(add_lines[, 1], log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(add_points[, 1], log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = log2(add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# }
# if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE &
# plot_horizontal == TRUE) {
# layout.matrix <- matrix(c(2, 1),
# nrow = 1,
# ncol = 2,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1),
# widths = c(10, 2.25))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(4, 0, 2, 5))
# image(
# y = seq(from = 0, to = n.levels),
# x = 1,
# z = (matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 4,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 4, 2, 0.5))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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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#' @title Plots an log2 spaced EHA spectra
#'
#' @description Plot wavelet scalogram using the outcome of the \code{\link{eha_log2}} function.
#'
#'@param eha_log2 eha_log2 object created using the \code{\link{eha_log2}} function.
#'@param plot_opt plot options are "Power", "Amplitude", "Probability" or "F_test"
#'@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}
#'@param pval_abline p value of the abline
#'@param pval_cutoff p value cutoff below which no data is displayed
#'
#' @return
#' The output is a plot of a EHA spectra.
#' if add_MTM_peaks = TRUE then the output of the MTM analysis will given as matrix
#'
#' @author
#' Code based on the wt.image" functions of the 'WaveletComp' R package
#' The EHA and MTM analysis parts are from the astrochron R package of Meyers et al., (2012)
#'
#' @references
#'Angi Roesch and Harald Schmidbauer (2018). WaveletComp: Computational
#'Wavelet Analysis. R package version 1.1.
#'\url{https://CRAN.R-project.org/package=WaveletComp}
#'
#'S.R. Meyers, 2012, Seeing Red in Cyclic Stratigraphy: Spectral Noise Estimation for
#'Astrochronology: Paleoceanography, 27, PA3228, <doi:10.1029/2012PA002307>
#'
#'S.R. Meyers, 2019 Cyclostratigraphy and the problem of astrochronologic testing, Earth-Science Reviews,
#'Volume 190, <doi.org/10.1016/j.earscirev.2018.11.015.>
#'
#'@examples
#' \donttest{
#'#Example 1. A plot of a wavelet spectra using the Total Solar Irradiance
#'# data set of Steinhilber et al., (2012)
#'
#'TSI_eha_log2 <- eha_log2(data = TSI,
#'win = 8192,
#'tbw = 4,
#'demean = TRUE,
#'detrend = TRUE,
#'upperPeriod = 8192,
#'lowerPeriod = 50,
#'pad = NULL,
#'padding = "noise")
#'
#'plot_eha_log2(
#'eha_log2 = TSI_eha_log2,
#'plot_opt = "Amplitude",
#'lowerPeriod = 50,
#'upperPeriod = 8192,
#'n.levels = 100,
#'palette_name = "rainbow",
#'color_brewer = "grDevices",
#'useRaster = TRUE,
#'periodlab = "Period (metres)",
#'x_lab = "depth (metres)",
#'keep_editable = FALSE,
#'dev_new = TRUE,
#'plot_dir = TRUE,
#'add_lines = NULL,
#'add_points = NULL,
#'add_abline_h = NULL,
#'add_abline_v = NULL,
#'add_MTM_peaks = FALSE,
#'add_data = TRUE,
#'add_avg = FALSE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal = TRUE)
#'
#'#Example 2. A plot of a wavelet spectra using the magnetic susceptibility
#'#data set of Pas et al., (2018)
#'mag_eha_log2 <- eha_log2(data = mag,
#'win = 50,
#'tbw = 4,
#'demean = TRUE,
#'detrend = TRUE,
#'upperPeriod = 50,
#'lowerPeriod = 1,
#'pad = NULL,
#'padding = "noise")
#'
#'plot_eha_log2(
#'eha_log2 = mag_eha_log2,
#'plot_opt = "Amplitude",
#'lowerPeriod = 1,
#'upperPeriod = 50,
#'n.levels = 100,
#'palette_name = "rainbow",
#'color_brewer = "grDevices",
#'useRaster = TRUE,
#'periodlab = "Period (metres)",
#'x_lab = "depth (metres)",
#'keep_editable = FALSE,
#'dev_new = TRUE,
#'plot_dir = TRUE,
#'add_lines = NULL,
#'add_points = NULL,
#'add_abline_h = NULL,
#'add_abline_v = NULL,
#'add_MTM_peaks = FALSE,
#'add_data = TRUE,
#'add_avg = FALSE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal = TRUE)
#'
#'
#'#Example 3. A plot of a wavelet spectra using the greyscale
#'# data set of Zeeden et al., (2013)
#'grey_eha_log2 <- eha_log2(data = grey,
#'win = 20,
#'tbw = 4,
#'demean = TRUE,
#'detrend = TRUE,
#'upperPeriod = 20,
#'lowerPeriod = 1,
#'pad = NULL,
#'padding = "noise")
#'
#'
#'plot_eha_log2(
#'eha_log2 = grey_eha_log2,
#'plot_opt = "Amplitude",
#'lowerPeriod = 1,
#'upperPeriod = 20,
#'n.levels = 100,
#'palette_name = "rainbow",
#'color_brewer = "grDevices",
#'useRaster = TRUE,
#'periodlab = "Period (metres)",
#'x_lab = "depth (metres)",
#'keep_editable = FALSE,
#'dev_new = TRUE,
#'plot_dir = TRUE,
#'add_lines = NULL,
#'add_points = NULL,
#'add_abline_h = NULL,
#'add_abline_v = NULL,
#'add_MTM_peaks = FALSE,
#'add_data = TRUE,
#'add_avg = FALSE,
#'add_MTM = FALSE,
#'mtm_siglvl = 0.95,
#'demean_mtm = TRUE,
#'detrend_mtm = TRUE,
#'padfac_mtm = 5,
#'tbw_mtm = 3,
#'plot_horizontal = TRUE)
#'}
#'
#' @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 astrochron mtm
#' @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_eha_log2 <- function (eha_log2 = NULL, plot_opt = "Amplitude", lowerPeriod = NULL,
upperPeriod = NULL, n.levels = 100, palette_name = "rainbow",
color_brewer = "grDevices", useRaster = TRUE, periodlab = "Period (metres)",
x_lab = "depth (metres)", keep_editable = FALSE, dev_new = TRUE,
plot_dir = TRUE, add_lines = NULL, add_points = NULL, add_abline_h = NULL,
add_abline_v = NULL, add_MTM_peaks = FALSE, add_data = TRUE,
add_avg = FALSE, pval_abline = c(0.1, 0.05), pval_cutoff = c(0.1),
add_MTM = FALSE, mtm_siglvl = 0.95, demean_mtm = TRUE, detrend_mtm = TRUE,
padfac_mtm = 5, tbw_mtm = 3, plot_horizontal = TRUE)
{
if (plot_opt == "Amplitude") {
mat <- eha_log2$amp
average <- eha_log2$amp.avg
}
else if (plot_opt == "Power") {
mat <- eha_log2$pwr
average <- eha_log2$pwr.avg
}
else if (plot_opt == "Probability") {
mat <- eha_log2$prob
average <- eha_log2$prob.avg
}
else if (plot_opt == "F_test") {
mat <- eha_log2$f_test
average <- eha_log2$f_test.avg
}
else {
mat <- eha_log2$amp
average <- eha_log2$amp.avg
}
if (keep_editable == FALSE) {
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
}
maximum.level = max(mat, na.rm = TRUE)
power_max_mat.levels = quantile(mat, na.rm = TRUE, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
if (color_brewer == "RColorBrewer") {
key.cols <- rev(colorRampPalette(brewer.pal(brewer.pal.info[palette_name,
1], palette_name))(n.levels))
}
if (color_brewer == "colorRamps") {
color_brewer_Sel <- paste("colorRamps::", palette_name,
"(n=n.levels)")
key.cols = eval(parse(text = color_brewer_Sel))
}
if (color_brewer == "grDevices") {
if (palette_name == "rainbow") {
color_brewer_Sel <- "grDevices::rainbow(n=n.levels, start = 0, end = 0.7)"
key.cols <- rev(eval(parse(text = color_brewer_Sel)))
}
else if (palette_name == "heat.colors" | palette_name ==
"terrain.colors" | palette_name == "topo.colors" |
palette_name == "cm.colors") {
color_brewer_Sel <- paste("grDevices::", palette_name,
"(n=n.levels, start = 0, end = 1)")
key.cols <- rev(eval(parse(text = color_brewer_Sel)))
}
else {
key.cols <- hcl.colors(n = n.levels, palette = palette_name,
alpha = NULL, rev = FALSE, fixup = TRUE)
}
}
if (color_brewer== "scico"){
color_brewer_Sel <- paste(
"scico::scico(n = n.levels, palette = '",
palette_name,
"', direction = -1)",
sep = ""
)
key.cols = rev(eval(parse(text = color_brewer_Sel)))
}
if (color_brewer == "viridis") {
color_brewer_Sel <- paste("viridis::", palette_name,
"(n=n.levels,direction = -1)")
key.cols = rev(eval(parse(text = color_brewer_Sel)))
}
periodtck = 0.02
periodtcl = 0.5
main = NULL
lwd = 2
lwd.axis = 1
legend.params = list(width = 1.2, shrink = 0.9, mar = 5.1,
n.ticks = 6, label.digits = 3, label.format = "f", lab = NULL,
lab.line = 2.5)
key.marks = round(seq(from = 0, to = 1, length.out = legend.params$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)
}
depth <- eha_log2$depth
y_axis <- eha_log2$log2_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(eha_log2$x, eha_log2$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(eha_log2$x, eha_log2$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(eha_log2$x), max(eha_log2$x)))
}
else {
xlim_vals = c(min(eha_log2$x), max(eha_log2$x))
}
if (is.null(lowerPeriod) == TRUE) {
lowerPeriod <- min(eha_log2$Period)
}
if (is.null(upperPeriod) == TRUE) {
upperPeriod <- max(eha_log2$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), widths = c(1, 4))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(4, 4, 2, 0))
plot(x = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, 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 = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = "", yaxt = "n",
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
period.tick = unique(trunc( as.numeric(eha_log2$log2_period)))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(1))
power_max_mat.levels = quantile(mat, 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 = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
}
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), widths = c(4, 1))
power_max_mat.levels = quantile(mat, 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 = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(as.numeric(eha_log2$log2_period)))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(4, 1))
power_max_mat.levels = quantile(mat, 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 = average, x = 2^eha_log2$log2_period, log = "x",
type = "l", xaxs = "i", xaxt = "n", ylab = "Wt. power",
xaxs = "i", xlim = ylim_vals)
par(new = FALSE, mar = c(4, 4, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(1, 2, 0, 3, 0, 4, 0, 5, 6,
7), nrow = 5, ncol = 2, byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
1, 1, 1, 4), widths = c(1, 4))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 1, 2, 6), xpd = FALSE)
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 1, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = mean(key.marks), line = 4,
font = par()$font.axis, cex = par()$cex.axis, las = 1)
box(lwd = lwd.axis)
par(mar = c(0, 0, 2, 2), xpd = FALSE)
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 2], type = "l",
xaxs = "i", xaxt = "n", ylab = "MTM power", xlab = "",
log = "x", xlim = ylim_vals)
for (i in 5:8) {
lines(x = 1/MTM_res_1[, 1], y = MTM_res_1[, i],
xlim = ylim_vals, lty = 3, col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(mar = c(0, 0, 0, 2), xpd = FALSE)
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 4], type = "l",
xaxs = "i", xaxt = "n", ylab = "", xlab = "", log = "x",
ylim = c(80, 101), xaxs = "i", xlim = ylim_vals)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
title(ylab = "Ar. conf lvl", xpd = NA)
plot(x = 1/MTM_res_1[, 1], y = MTM_res_1[, 3], type = "l",
xaxs = "i", xaxt = "n", ylab = "", xlab = "", log = "xy",
ylim = c(80, 101), yaxs = "i", xlim = ylim_vals)
title(ylab = "Har. conf lvl", xpd = NA)
abline(h = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = average, x = 2^eha_log2$log2_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 = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, xaxt = "n",
yaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(as.numeric(eha_log2$log2_period)))
period.tick[period.tick < log2(as.numeric(eha_log2$log2_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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE &
plot_horizontal == FALSE) {
layout.matrix <- matrix(c(1, 2, 3, 4), nrow = 2, ncol = 2,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1,
4), widths = c(1, 4))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(2, 0.5, 2, 6), xpd = NA)
image(y = seq(from = 0, to = n.levels), x = 1, z = (matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(2, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 2, at = key.marks, line = 0.5,
las = 2, font = par()$font.axis, cex = par()$cex.axis)
mtext(c("Power"), side = 1, at = 1, line = 0.5, font = par()$font.axis,
cex = par()$cex.axis, las = 1, xpd = NA)
box(lwd = lwd.axis)
par(mar = c(0, 0, 2, 2))
plot(y = average, x = 2^eha_log2$log2_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 = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
par(new = FALSE, mar = c(4, 0, 0, 2), xpd = FALSE)
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = "", xaxt = "n",
yaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(1, 4))
power_max_mat.levels = quantile(mat, 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 = eha_log2$y, y = eha_log2$x, type = "l", yaxs = "i",
xlab = "proxy value", ylab = x_lab, ylim = xlim_vals)
par(new = FALSE, mar = c(4, 0, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, xaxt = "n",
yaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(1, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$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), widths = c(1, 4))
power_max_mat.levels = quantile(mat, 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 = average, x = 2^eha_log2$log2_period, log = "x",
type = "l", xaxs = "i", xaxt = "n", ylab = "Wt. power",
xaxs = "i", xlim = ylim_vals)
if (is.null(add_abline_v) != TRUE) {
abline(v = (add_abline_v))
}
par(new = FALSE, mar = c(4, 4, 0, 2))
image(y = eha_log2$depth, x = eha_log2$log2_period,
z = (mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, xlab = periodlab, ylab = x_lab,
xaxt = "n", main = main, ylim = xlim_vals, xlim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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)
mtext(period.tick.label, side = 1, at = period.tick,
las = 2, line = par()$mgp[2] - 0.5, font = par()$font.axis,
cex = par()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(y = add_lines[,
1], x = log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(y = add_points[,
1], x = log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(v = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = (add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = log2(add_abline_v))
}
}
if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(1, 1, 1, 1, 1, 1, 2, 2, 2,
3, 3, 3, 3, 3, 3, 4, 5, 6), nrow = 2, ncol = 9,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(0.25,
1), widths = c(1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 0))
plot(y = eha_log2$y, x = eha_log2$x, type = "l", xaxs = "i",
xlab = "", ylab = "proxy value", xaxt = "n", xlim = xlim_vals)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(3, 2, 2, 2), mgp = c(2, 1,
0))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "Power",
ylab = "")
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2)
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex = 0.75)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 0, 0), mgp = c(2, 1,
0))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 2], type = "l",
yaxs = "i", yaxt = "n", xlab = "MTM power", ylab = "",
log = "y", ylim = ylim_vals)
for (i in 5:8) {
lines(y = 1/MTM_res_1[, 1], x = MTM_res_1[, i],
ylim = ylim_vals, lty = 3, col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 4], type = "l",
yaxs = "i", yaxt = "n", xlab = "Ar. conf lvl", ylab = "",
log = "y", xlim = c(80, 101), xaxs = "i", ylim = ylim_vals)
abline(v = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 3], type = "l",
yaxs = "i", yaxt = "n", xlab = "Har. conf lvl",
ylab = "", log = "xy", xlim = c(80, 101), xaxs = "i",
ylim = ylim_vals)
abline(v = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
}
if (add_data == TRUE & add_avg == TRUE & add_MTM == FALSE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(1, 2, 4, 3), nrow = 2, ncol = 2,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(0.25,
1), widths = c(8, 2))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 0))
plot(y = eha_log2$y, x = eha_log2$x, type = "l", xaxs = "i",
xlab = "", ylab = "proxy value", xaxt = "n", xlim = xlim_vals)
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
par(new = FALSE, mar = c(3, 2, 2, 2), mgp = c(2, 1,
0))
image(x = seq(from = 0, to = n.levels), y = 1, z = t(matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "Power",
ylab = "")
axis(1, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.2)
mtext(key.labels, side = 1, at = key.marks, line = 0.1,
las = 2, cex = 0.75)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 0, 0.5))
plot(x = average, y = 2^eha_log2$log2_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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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), widths = c(8, 2))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 2))
plot(y = eha_log2$y, x = eha_log2$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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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), widths = c(1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(0, 4, 2, 0))
plot(y = eha_log2$y, x = eha_log2$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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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 = average, y = 2^eha_log2$log2_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),
widths = c(6, 1, 1))
power_max_mat.levels = quantile(mat, 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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(x = average, y = 2^eha_log2$log2_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 = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), 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))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
period.tick = na.omit(period.tick)
period.tick.label = 2^(period.tick)
axis(2, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
axis(4, lwd = lwd.axis, at = period.tick, labels = NA,
tck = periodtck, tcl = periodtcl)
mtext(period.tick.label, side = 2, at = period.tick,
las = 2, line = par()$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),
widths = c(6, 1, 1, 1, 1, 1))
power_max_mat.levels = quantile(mat, 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 = average, y = 2^eha_log2$log2_period, log = "y",
type = "l", yaxs = "i", yaxt = "n", xlab = "Wt. power",
xaxs = "i", ylim = ylim_vals)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "black", lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = add_abline_h)
}
par(new = FALSE, mar = c(4, 4, 2, 0), mgp = c(2, 1,
0))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(5, 4, 3, 2, 1), nrow = 1,
ncol = 5, byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1),
widths = c(7, 1, 1, 1, 1))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(4, 0, 2, 5))
image(y = seq(from = 0, to = n.levels), x = 1, z = (matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 0, 2, 0.5))
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 3], type = "l",
yaxs = "i", yaxt = "n", xlab = "Har. conf lvl",
ylab = "", log = "xy", xlim = c(80, 101), xaxs = "i",
ylim = ylim_vals)
abline(v = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 4], type = "l",
yaxs = "i", yaxt = "n", xlab = "Ar. conf lvl", ylab = "",
log = "y", xlim = c(80, 101), xaxs = "i", ylim = ylim_vals)
abline(v = c(90, 95, 99), lty = 3, col = "grey", lwd = 2)
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
plot(y = 1/MTM_res_1[, 1], x = MTM_res_1[, 2], type = "l",
yaxs = "i", yaxt = "n", xlab = "MTM power", ylab = "",
log = "y", ylim = ylim_vals)
for (i in 5:8) {
lines(y = 1/MTM_res_1[, 1], x = MTM_res_1[, i],
ylim = ylim_vals, lty = 3, col = "grey", lwd = 2)
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = 1/MTM_res_2[, 1], col = "red", lty = 3)
}
par(new = FALSE, mar = c(4, 4, 2, 0), mgp = c(2, 1,
0))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE &
plot_horizontal == TRUE) {
layout.matrix <- matrix(c(2, 1), nrow = 1, ncol = 2,
byrow = TRUE)
graphics::layout(mat = layout.matrix, heights = c(1),
widths = c(10, 2.25))
power_max_mat.levels = quantile(mat, probs = seq(from = 0,
to = 1, length.out = n.levels + 1))
par(mar = c(4, 0, 2, 5))
image(y = seq(from = 0, to = n.levels), x = 1, z = (matrix(power_max_mat.levels,
nrow = 1)), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, yaxt = "n", xaxt = "n", xlab = "",
ylab = "", )
axis(4, lwd = lwd.axis, at = key.marks, labels = NA,
tck = 0.02, tcl = 1.24)
mtext(key.labels, side = 4, at = key.marks, line = 0.5,
las = 2, font = par()$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()$cex.axis)
box(lwd = lwd.axis)
par(new = FALSE, mar = c(4, 4, 2, 0.5))
image(x = eha_log2$depth, y = eha_log2$log2_period,
z = t(mat), col = key.cols, breaks = power_max_mat.levels,
useRaster = TRUE, ylab = periodlab, xlab = x_lab,
axes = TRUE, yaxt = "n", main = main, xlim = xlim_vals,
ylim = log2(ylim_vals))
box(lwd = lwd.axis)
period.tick = unique(trunc(eha_log2$log2_period))
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()$cex.axis)
if (is.null(add_lines) != TRUE) {
for (i in 2:ncol(add_lines)) lines(add_lines[, 1],
log2(add_lines[, i]))
}
if (is.null(add_points) != TRUE) {
for (i in 2:ncol(add_points)) points(add_points[,
1], log2(add_points[, i]))
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
FALSE) {
abline(h = log2(1/MTM_res_2[, 1]), col = "black",
lty = 3)
}
if (is.null(add_abline_h) != TRUE) {
abline(h = log2(add_abline_h))
}
if (is.null(add_abline_v) != TRUE) {
abline(v = add_abline_v)
}
}
if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) == FALSE) {
return(invisible(mtm_res))
}
}
### old function keep for now #
#
# plot_eha_log2 <- function (eha_log2 = NULL,
# plot_opt = "Amplitude",
# lowerPeriod = NULL,
# upperPeriod = NULL,
# n.levels = 100,
# palette_name = "rainbow",
# color_brewer = "grDevices",
# useRaster = TRUE,
# periodlab = "Period (metres)",
# x_lab = "depth (metres)",
# keep_editable = FALSE,
# dev_new = TRUE,
# plot_dir = TRUE,
# add_lines = NULL,
# add_points = NULL,
# add_abline_h = NULL,
# add_abline_v = NULL,
# add_MTM_peaks = FALSE,
# add_data = TRUE,
# add_avg = FALSE,
# pval_abline = c(0.1, 0.05),
# pval_cutoff = c(0.1),
# add_MTM = FALSE,
# mtm_siglvl = 0.95,
# demean_mtm = TRUE,
# detrend_mtm = TRUE,
# padfac_mtm = 5,
# tbw_mtm = 3,
# plot_horizontal = TRUE)
# {
# if (plot_opt == "Amplitude") {
# mat <- eha_log2$amp
# average <- eha_log2$amp.avg} else if (plot_opt == "Power") {
# mat <- eha_log2$pwr
# average <- eha_log2$pwr.avg} else if (plot_opt == "Probability") {
# mat <- eha_log2$prob
# average <- eha_log2$prob.avg} else if (plot_opt == "F_test") {
# mat <- eha_log2$f_test
# average <- eha_log2$f_test.avg} else{
# mat <- eha_log2$amp
# average <- eha_log2$amp.avg
# }
#
#
# if (keep_editable == FALSE) {
# oldpar <- par(no.readonly = TRUE)
# on.exit(par(oldpar))
# }
# maximum.level = max(mat,na.rm=TRUE)
# power_max_mat.levels = quantile(mat,na.rm=TRUE, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# if (color_brewer == "RColorBrewer") {
# key.cols <- rev(colorRampPalette(brewer.pal(brewer.pal.info[palette_name, 1], palette_name))(n.levels))
# }
# if (color_brewer == "colorRamps") {
# color_brewer_Sel <- paste("colorRamps::", palette_name, "(n=n.levels)")
# key.cols = eval(parse(text = color_brewer_Sel))
# }
# if (color_brewer == "grDevices") {
# if (palette_name == "rainbow") {
# color_brewer_Sel <- "grDevices::rainbow(n=n.levels, start = 0, end = 0.7)"
# key.cols <- rev(eval(parse(text = color_brewer_Sel)))
# }
# else if (palette_name == "heat.colors" | palette_name ==
# "terrain.colors" | palette_name == "topo.colors" |
# palette_name == "cm.colors") {
# color_brewer_Sel <- paste("grDevices::",
# palette_name,
# "(n=n.levels, start = 0, end = 1)")
# key.cols <- rev(eval(parse(text = color_brewer_Sel)))
# }
# else {
# key.cols <- hcl.colors(
# n = n.levels,
# palette = palette_name,
# alpha = NULL,
# rev = FALSE,
# fixup = TRUE
# )
# }
# }
# if (color_brewer == "viridis") {
# color_brewer_Sel <- paste("viridis::", palette_name, "(n=n.levels,direction = -1)")
# key.cols = rev(eval(parse(text = color_brewer_Sel)))
# }
# periodtck = 0.02
# periodtcl = 0.5
# main = NULL
# lwd = 2
# lwd.axis = 1
# legend.params = list(
# width = 1.2,
# shrink = 0.9,
# mar = 5.1,
# n.ticks = 6,
# label.digits = 3,
# label.format = "f",
# lab = NULL,
# lab.line = 2.5
# )
# key.marks = round(seq(
# from = 0,
# to = 1,
# length.out = legend.params$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)
# }
#
# depth <- eha_log2$depth
# y_axis <- eha_log2$log2_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(eha_log2$x, eha_log2$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(eha_log2$x, eha_log2$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(eha_log2$x), max(eha_log2$x)))
# }else {
# xlim_vals = c(min(eha_log2$x), max(eha_log2$x))
# }
# if (is.null(lowerPeriod) == TRUE) {
# lowerPeriod <- min(eha_log2$Period)
# }
# if (is.null(upperPeriod) == TRUE) {
# upperPeriod <- max(eha_log2$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),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(4, 4, 2, 0))
# plot(
# x = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# 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 = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = "",
# yaxt = "n",
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# period.tick = unique(trunc(eha_log2$log2_period))
# #period.tick[period.tick < log2(eha_log2$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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
#
# if (add_data == FALSE & add_avg == FALSE & add_MTM == FALSE &
# plot_horizontal == FALSE) {
# #graphics.off()
# layout.matrix <- matrix(c(1, 2),
# nrow = 2,
# ncol = 1,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1, 4),
# widths = c(1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(2, 4, 2, 3))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 4, 2, 3))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# }
# if (add_data == FALSE & add_avg == FALSE & add_MTM == TRUE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(
# c(2, 1, 3, 0, 4, 0, 5, 0),
# nrow = 4,
# ncol = 2,
# byrow = TRUE
# )
# graphics::layout(mat = layout.matrix,
# heights = c(1, 1, 1, 4),
# widths = c(4, 1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(2, 2, 2, 3))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(mar = c(0, 4, 2, 2))
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 2],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "MTM power",
# xlab = "",
# log = "x",
# xlim = ylim_vals
# )
# for (i in 5:8) {
# lines(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, i],
# xlim = ylim_vals,
# lty = 3,
# col = "grey",
# lwd = 2
# )
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(mar = c(0, 4, 0, 2))
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 4],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Ar. conf lvl",
# xlab = "",
# log = "x",
# ylim = c(80, 101),
# xaxs = "i",
# xlim = ylim_vals
# )
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 3],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Har. conf lvl",
# xlab = "",
# log = "xy",
# ylim = c(80, 101),
# yaxs = "i",
# xlim = ylim_vals
# )
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(new = FALSE, mar = c(4, 4, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
#
# if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(
# c(2, 1, 3, 0, 4, 0, 5, 0, 6, 0),
# nrow = 5,
# ncol = 2,
# byrow = TRUE
# )
# graphics::layout(
# mat = layout.matrix,
# heights = c(1, 1, 1, 1, 4),
# widths = c(4, 1)
# )
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(2, 2, 2, 3))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(mar = c(0, 4, 2, 2))
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 2],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "MTM power",
# xlab = "",
# log = "x",
# xlim = ylim_vals
# )
# for (i in 5:8) {
# lines(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, i],
# xlim = ylim_vals,
# lty = 3,
# col = "grey",
# lwd = 2
# )
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(mar = c(0, 4, 0, 2))
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 4],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Ar. conf lvl",
# xlab = "",
# log = "x",
# ylim = c(80, 101),
# xaxs = "i",
# xlim = ylim_vals
# )
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 3],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Har. conf lvl",
# xlab = "",
# log = "xy",
# ylim = c(80, 101),
# yaxs = "i",
# xlim = ylim_vals
# )
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
#
# plot(
# y = average,
# x = 2^eha_log2$log2_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 = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(1, 4)
# )
# power_max_mat.levels = quantile(mat, 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 = average,
# x = 2^eha_log2$log2_period,
# log = "x",
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Wt. power",
# xaxs = "i",
# xlim = ylim_vals
# )
# title(ylab = "Wt. power", xpd = NA)
# par(mar = c(4, 4, 0, 0), xpd = FALSE)
# plot(
# x = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# par(new = FALSE, mar = c(4, 0, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# xaxt = "n",
# yaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$axis.2))
# period.tick[period.tick < log2(eha_log2$Period[1])] = NA
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, 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 = average,
# x = 2^eha_log2$log2_period,
# log = "x",
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "Wt. power",
# xlab = "",
# xaxs = "i",
# xlim = ylim_vals
# )
# title(ylab = "Wt. power", xpd = NA)
# par(mar = c(4, 4, 0, 0), xpd = TRUE)
# plot(
# x = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# par(new = FALSE,
# mar = c(4, 0, 0, 2),
# xpd = FALSE)
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = "",
# xaxt = "n",
# yaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
# if (add_data == TRUE & add_avg == FALSE & add_MTM == TRUE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(
# c(1, 2, 0, 3, 0, 4, 5, 6),
# nrow = 4,
# ncol = 2,
# byrow = TRUE
# )
# graphics::layout(mat = layout.matrix,
# heights = c(1, 1, 1, 4),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 1, 2, 6), xpd = NA)
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# mtext(
# c("Power"),
# side = 1,
# at = mean(key.marks),
# line = 4,
# font = par()$font.axis,
# cex = par()$cex.axis,
# las = 1
# )
# box(lwd = lwd.axis)
# par(mar = c(0, 0, 2, 2))
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 2],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "MTM power",
# xlab = "",
# log = "x",
# xlim = ylim_vals
# )
# for (i in 5:8) {
# lines(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, i],
# xlim = ylim_vals,
# lty = 3,
# col = "grey",
# lwd = 2
# )
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(mar = c(0, 0, 0, 2), xpd = FALSE)
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 4],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "",
# xlab = "",
# log = "x",
# ylim = c(80, 101),
# xaxs = "i",
# xlim = ylim_vals
# )
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# title(ylab = "Ar. conf lvl", xpd = NA)
# plot(
# x = 1 / MTM_res_1[, 1],
# y = MTM_res_1[, 3],
# type = "l",
# xaxs = "i",
# xaxt = "n",
# ylab = "",
# xlab = "",
# log = "xy",
# ylim = c(80, 101),
# yaxs = "i",
# xlim = ylim_vals
# )
# title(ylab = "Har. conf lvl", xpd = NA)
# abline(
# h = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# par(mar = c(4, 4, 0, 0))
# plot(
# x = eha_log2$y,
# y = eha_log2$x,
# type = "l",
# yaxs = "i",
# xlab = "proxy value",
# ylab = x_lab,
# ylim = xlim_vals
# )
# par(new = FALSE, mar = c(4, 0, 0, 2))
# image(
# y = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# xaxt = "n",
# yaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$mgp[2] - 0.5,
# font = par()$font.axis,
# cex = par()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(y = add_lines[, 1], x = log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(y = add_points[, 1], x = log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(v = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = (add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = log2(add_abline_v))
# }
# }
# if (add_data == FALSE & add_avg == TRUE & add_MTM == FALSE &
# plot_horizontal == FALSE) {
# layout.matrix <- matrix(c(1, 2, 0, 3),
# nrow = 2,
# ncol = 2,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(1, 4),
# widths = c(1, 4))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(2, 2, 2, 3))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis,
# xpd = NA
# )
# box(lwd = lwd.axis)
# par(mar = c(0, 4, 2, 2))
# plot(
# y = average,
# x = 2^eha_log2$log2_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 = eha_log2$depth,
# x = eha_log2$log2_period,
# z = (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# xlab = periodlab,
# ylab = x_lab,
# xaxt = "n",
# main = main,
# ylim = xlim_vals,
# xlim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 1,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 1,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 0))
# plot(
# y = eha_log2$y,
# x = eha_log2$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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(8, 2))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 0))
# plot(
# y = eha_log2$y,
# x = eha_log2$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 = average,
# y = 2^eha_log2$log2_period,
# log = "y",
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Wt. power",
# xaxs = "i",
# ylim = ylim_vals
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = add_abline_h)
# }
# par(new = FALSE,
# mar = c(4, 4, 0, 0),
# xpd = FALSE)
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(add_lines[, 1], log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(add_points[, 1], log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = log2(add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# }
# if (add_data == TRUE & add_avg == FALSE & add_MTM == FALSE &
# plot_horizontal == TRUE) {
# layout.matrix <- matrix(c(1, 0, 3, 2),
# nrow = 2,
# ncol = 2,
# byrow = TRUE)
# graphics::layout(mat = layout.matrix,
# heights = c(0.25, 1),
# widths = c(8, 2))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 2))
# plot(
# y = eha_log2$y,
# x = eha_log2$x,
# type = "l",
# xaxs = "i",
# xlab = "",
# ylab = "proxy value",
# xaxt = "n",
# xlim = xlim_vals
# )
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# par(new = FALSE, mar = c(4, 0, 2, 5))
# image(
# y = seq(from = 0, to = n.levels),
# x = 1,
# z = (matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 4,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 4, 0, 2))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(add_lines[, 1], log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(add_points[, 1], log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = log2(add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# }
# if (add_data == TRUE & add_avg == TRUE & add_MTM == TRUE &
# plot_horizontal == TRUE) {
# layout.matrix <- matrix(
# c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 5, 6, 7),
# nrow = 2,
# ncol = 10,
# byrow = TRUE
# )
# graphics::layout(mat = layout.matrix,
# heights = c(0.25, 1),
# widths = c(1))
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(0, 4, 2, 0))
# plot(
# y = eha_log2$y,
# x = eha_log2$x,
# type = "l",
# xaxs = "i",
# xlab = "",
# ylab = "proxy value",
# xaxt = "n",
# xlim = xlim_vals
# )
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# par(new = FALSE,
# mar = c(3, 2, 2, 2),
# mgp = c(2, 1, 0))
# image(
# x = seq(from = 0, to = n.levels),
# y = 1,
# z = t(matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "Power",
# ylab = ""
# )
# axis(
# 1,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.2
# )
# mtext(
# key.labels,
# side = 1,
# at = key.marks,
# line = 0.1,
# las = 2,
# cex = 0.75
# )
# box(lwd = lwd.axis)
# par(new = FALSE,
# mar = c(4, 4, 0, 0),
# mgp = c(2, 1, 0))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(add_lines[, 1], log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(add_points[, 1], log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = log2(add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# par(new = FALSE, mar = c(4, 0, 0, 0.5))
# plot(
# x = average,
# y = 2^eha_log2$log2_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),
# widths = c(6, 1, 1))
# power_max_mat.levels = quantile(mat, 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 = average,
# y = 2^eha_log2$log2_period,
# log = "y",
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Wt. power",
# xaxs = "i",
# ylim = ylim_vals
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = add_abline_h)
# }
# par(new = FALSE,
# mar = c(4, 4, 2, 0),
# mgp = c(2, 1, 0))
# image(
# x = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# ylab = periodlab,
# xlab = x_lab,
# axes = TRUE,
# yaxt = "n",
# main = main,
# xlim = xlim_vals,
# ylim = log2(ylim_vals)
# )
#
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# 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()$cex.axis
# )
# if (is.null(add_lines) != TRUE) {
# for (i in 2:ncol(add_lines))
# lines(add_lines[, 1], log2(add_lines[, i]))
# }
# if (is.null(add_points) != TRUE) {
# for (i in 2:ncol(add_points))
# points(add_points[, 1], log2(add_points[, i]))
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = log2(1 / MTM_res_2[, 1]),
# col = "black",
# lty = 3)
# }
# if (is.null(add_abline_h) != TRUE) {
# abline(h = log2(add_abline_h))
# }
# if (is.null(add_abline_v) != TRUE) {
# abline(v = add_abline_v)
# }
# }
# if (add_data == FALSE & add_avg == TRUE & add_MTM == TRUE &
# plot_horizontal == TRUE) {
# layout.matrix <- matrix(c(6, 5, 4, 3, 2, 1),
# nrow = 1,
# ncol = 6,
# byrow = TRUE)
# graphics::layout(
# mat = layout.matrix,
# heights = c(1),
# widths = c(6, 1, 1, 1, 1, 1)
# )
# power_max_mat.levels = quantile(mat, probs = seq(
# from = 0,
# to = 1,
# length.out = n.levels + 1
# ))
# par(mar = c(4, 0, 2, 5))
# image(
# y = seq(from = 0, to = n.levels),
# x = 1,
# z = (matrix(power_max_mat.levels, nrow = 1)),
# col = key.cols,
# breaks = power_max_mat.levels,
# useRaster = TRUE,
# yaxt = "n",
# xaxt = "n",
# xlab = "",
# ylab = "",
#
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = key.marks,
# labels = NA,
# tck = 0.02,
# tcl = 1.24
# )
# mtext(
# key.labels,
# side = 4,
# at = key.marks,
# line = 0.5,
# las = 2,
# font = par()$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()$cex.axis
# )
# box(lwd = lwd.axis)
# par(new = FALSE, mar = c(4, 0, 2, 0.5))
# plot(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, 3],
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Har. conf lvl",
# ylab = "",
# log = "xy",
# xlim = c(80, 101),
# xaxs = "i",
# ylim = ylim_vals
# )
# abline(
# v = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, 4],
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "Ar. conf lvl",
# ylab = "",
# log = "y",
# xlim = c(80, 101),
# xaxs = "i",
# ylim = ylim_vals
# )
# abline(
# v = c(90, 95, 99),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, 2],
# type = "l",
# yaxs = "i",
# yaxt = "n",
# xlab = "MTM power",
# ylab = "",
# log = "y",
# ylim = ylim_vals
# )
# for (i in 5:8) {
# lines(
# y = 1 / MTM_res_1[, 1],
# x = MTM_res_1[, i],
# ylim = c(min(y_axis), max(y_axis)),
# lty = 3,
# col = "grey",
# lwd = 2
# )
# }
# if (add_MTM_peaks == TRUE & is.na(MTM_res_2[1, 2]) ==
# FALSE) {
# abline(h = 1 / MTM_res_2[, 1],
# col = "red",
# lty = 3)
# }
# plot(
# x = average,
# y = 2^eha_log2$log2_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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(7, 1, 1, 1, 1))
# power_max_mat.levels = quantile(mat, 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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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),
# widths = c(10, 2.25))
# power_max_mat.levels = quantile(mat, 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 = eha_log2$depth,
# y = eha_log2$log2_period,
# z =t (mat),
# 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)
# )
# box(lwd = lwd.axis)
# period.tick = unique(trunc(eha_log2$log2_period))
# period.tick = na.omit(period.tick)
# period.tick.label = 2^(period.tick)
# axis(
# 2,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# axis(
# 4,
# lwd = lwd.axis,
# at = period.tick,
# labels = NA,
# tck = periodtck,
# tcl = periodtcl
# )
# mtext(
# period.tick.label,
# side = 2,
# at = period.tick,
# las = 2,
# line = par()$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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