R/plot_prh_fig2_m2.R

In tagtools: Work with Data from High-Resolution Biologging Tags

#' Plot second detail (one-dive) plot for prh_predictor method 2
#'
#' This is an internal function used by prh_predictor. It plots the second figure window.
#' @param A 3-column Acceleration data matrix (columns are x, y, z in tag frame)
#' @param v a vector of vertical speeds (same number of rows as A)
#' @param sampling_rate Sampling rate of A in Hz
#' @param seg information about which segments of data to plot. A one-row matrix with 2 columns: start end end times of box
#' @param prh one row of PRH info (start time, p0, r0, h0, quality) for the segment seg
#' @param prompt Main title for top panel (prompt for user interaction)
#' @noRd
#'
plot_prh_fig2_m2 <- function(A, v, sampling_rate, seg, prh, prompt) {
  oldpar <- graphics::par(no.readonly = TRUE)
  on.exit(graphics::par(oldpar))
  
  #*****************************************
  # colors for PRH data
  #*****************************************
  rgb_cols <- matrix(c(
    0, 0.4470, 0.7410,
    0.85, 0.3250, 0.098,
    0.9290, 0.6940, 0.1250
  ),
  nrow = 3, byrow = TRUE
  )
  hex_cols <- grDevices::rgb(
    red = rgb_cols[, 1],
    green = rgb_cols[, 2],
    blue = rgb_cols[, 3]
  )
  names(hex_cols) <- c("p", "r", "h")

  YEXT <- 12.5 # vertical extent of accelerometry plots +/-m/s^2
  # x limits
  xl2 <- seg + c(-30, 30)
  # accel data in whale frame according to current prh values
  Aw <- A %*% t(euler2rotmat(prh[2], prh[3], prh[4]))

  # top plot
  graphics::par(mfrow = c(2, 1), mar = c(4, 5, 3, 1))
  graphics::plot(c(1:nrow(A)) / sampling_rate, A[, 1] * 9.81,
    type = "l", col = hex_cols[1],
    xlim = xl2, ylim = c(YEXT * c(-1, 1)),
    xaxt = "n",
    main = prompt,
    xlab = "", ylab = latex2exp::TeX("Tag frame A, m/s^2")
  )
  # add x axis with no tick labels
  graphics::axis(side = 1, labels = FALSE)
  for (col in c(2:3)) {
    graphics::lines(c(1:nrow(A)) / sampling_rate, A[, col] * 9.81,
      type = "l", col = hex_cols[col]
    )
  }
  graphics::grid()
  graphics::legend("bottomright",
    bty = "n", legend = names(hex_cols),
    text.col = hex_cols, horiz = TRUE
  )
  # add box
  graphics::rect(
    xleft = seg[1], xright = seg[2],
    ybottom = -0.9 * YEXT, ytop = 0.9 * YEXT,
    border = "black"
  )

  # bottom panel
  # need to convert from matlab
  msg <- paste(
    "At ", round(prh[1]), ", ",
    "p0 = ", round(prh[2] * 180 / pi, digits = 1), ", ",
    "r0 = ", round(prh[3] * 180 / pi, digits = 1), ", ",
    "h0 = ", round(prh[4] * 180 / pi, digits = 1), ", ",
    "Quality: ", round(prh[5], digits = 3)
  )

  graphics::plot(c(1:nrow(Aw)) / sampling_rate, Aw[, 1] * 9.81,
    type = "l", col = hex_cols[1],
    xlim = xl2, ylim = c(YEXT * c(-1, 1)),
    xlab = "", ylab = latex2exp::TeX("Animal frame A, m/s^2"),
    main = msg
  )
  for (col in c(2:3)) {
    graphics::lines(c(1:nrow(Aw)) / sampling_rate, Aw[, col] * 9.81,
      type = "l", col = hex_cols[col]
    )
  }
  graphics::grid()
  # add boxes
  graphics::rect(
    xleft = seg[1], xright = seg[2],
    ybottom = -0.9 * YEXT, ytop = 0.9 * YEXT,
    border = "black"
  )
} # end of plot_fig2