R/plottingfunctions.R

In AvInertia: Calculate the Inertial Properties of a Flying Bird

# This script contains all applicable plotting functions

#' Plot the center of gravity of each component
#'
#' @param clean_pts Dataframe of the key positions of the bird as follows:
#' \itemize{
#' \item{pt1x, pt1y, pt1z}{Point on the shoulder joint}
#' \item{pt2x, pt1y, pt2z}{Point on the elbow joint}
#' \item{pt3x, pt3y, pt3z}{Point on the wrist joint}
#' \item{pt4x, pt4y, pt4z}{Point on the end of carpometacarpus}
#' \item{pt6x, pt6y, pt6z}{Point on the leading edge of the wing in front of the
#' wrist joint}
#' \item{pt8x, pt8y, pt8z}{Point on tip of most distal primary}
#' \item{pt9x, pt9y, pt9z}{Point that defines the end of carpometacarpus}
#' \item{pt10x, pt10y, pt10z}{Point on tip of last primary to model as if on the
#' end of the carpometacarpus}
#' \item{pt11x, pt11y, pt11z}{Point on tip of most proximal feather
#' (wing root trailing edge)}
#' \item{pt12x, pt12y, pt12z}{Point on exterior shoulder position
#' (wing root leading edge)}
#' }
#' @param mass_properties Dataframe containing the center of gravity and
#' moment of inertia components of the full wing.
#' @param mass_properties_skin Dataframe containing the center of gravity and
#' moment of inertia components of the skin.
#' Formatted with the following columns: "species","BirdID","TestID","FrameID",
#' "prop_type","component","value".
#' @param mass_properties_bone Dataframe containing the center of gravity and
#' moment of inertia components of the wing bones.
#' Formatted with the following columns: "species","BirdID","TestID","FrameID",
#' "prop_type","component","value".
#' @param mass_properties_feathers Dataframe containing the center of gravity and
#' moment of inertia components of the feathers.
#' Formatted with the following columns: "species","BirdID","TestID","FrameID",
#' "prop_type","component","value".
#' @param mass_properties_muscle Dataframe containing the center of gravity and
#' moment of inertia components of the muscles
#' Formatted with the following columns: "species","BirdID","TestID","FrameID",
#' "prop_type","component","value".
#' @param prop_tertiary1 Dataframe containing the center of gravity and
#' moment of inertia components of the first tertiary group.
#' Formatted with the following columns: "species","BirdID","TestID","FrameID",
#' "prop_type","component","value".
#' @param prop_tertiary2 Dataframe containing the center of gravity and
#' moment of inertia components of the second tertiary group.
#' Formatted with the following columns: "species","BirdID","TestID","FrameID",
#' "prop_type","component","value".
#' @param plot_var Character of either "yx" or "yz".
#' Defines the output axes of the plot.
#'
#' @return A plot of the request axes
#'
#' @inherit combine_inertialprop examples
#'
#' @export
#'

plot_CGloc <-
  function(clean_pts,
           mass_properties,
           mass_properties_skin,
           mass_properties_bone,
           mass_properties_feathers,
           mass_properties_muscle,
           prop_tertiary1,
           prop_tertiary2,
           plot_var) {
    # Set variables to NULL to avoid having to define as a global variable as
    # CRAN can't see a binding for feather within the dataframe dat_feat_curr
    component=NULL
    object=NULL
    primaries   = mass_properties_feathers[grep("P", mass_properties_feathers$component), ]
    secondaries = mass_properties_feathers[grep("S", mass_properties_feathers$component), ]


    #--- Predefine the main theme ----
    th <- ggplot2::theme_classic() +
      ggplot2::theme(
        # Text
        axis.title  = ggplot2::element_text(size = 10),
        axis.text   = ggplot2::element_text(size = 10, colour = "black"),
        axis.text.x.top = ggplot2::element_text(margin = ggplot2::margin(t = 0, r = 0, b = 0, l = 0), vjust = 3.5),
        axis.text.y = ggplot2::element_text(margin = ggplot2::margin(r = 10)),
        # Axis line
        axis.line   = ggplot2::element_blank(),
        axis.ticks.length = ggplot2::unit(-5, "pt"),
        # Legend
        legend.position  = 'none',
        # Background transparency
        # Background of panel
        panel.background = ggplot2::element_rect(fill = "transparent"),
        # Background behind actual data points
        plot.background  = ggplot2::element_rect(fill = "transparent", color = NA)
      )

    CGplot_x <- ggplot2::ggplot() +
      # Add in data
      ggplot2::geom_point(
        ggplot2::aes(x = prop_tertiary1$CG[2], y = prop_tertiary1$CG[1]),
        col = "black",
        fill = "#BEA4BD",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(x = prop_tertiary2$CG[2], y = prop_tertiary2$CG[1]),
        col = "black",
        fill = "#BEA4BD",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties_skin, object == "CGy")$value,
          y = subset(mass_properties_skin, object == "CGx")$value
        ),
        col = "black",
        fill = "#BEA4BD",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties_bone, object == "CGy")$value,
          y = subset(mass_properties_bone, object == "CGx")$value
        ),
        col = "black",
        fill = "#FAC5C6",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(primaries, object == "CGy")$value,
          y = subset(primaries, object == "CGx")$value
        ),
        col = "black",
        fill = "#A0B3DC",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(secondaries, object == "CGy")$value,
          y = subset(secondaries, object == "CGx")$value
        ),
        col = "black",
        fill = "#9AD09B",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties_muscle, object == "CGy")$value,
          y = subset(mass_properties_muscle, object == "CGx")$value
        ),
        col = "black",
        fill = "#FAC5C6",
        pch = 21
      ) +
      ggplot2::geom_point(ggplot2::aes(
        x = subset(mass_properties, component == "wing" &
                     object == "CGy")$value,
        y = subset(mass_properties, component == "wing" &
                     object == "CGx")$value
      ),
      col = "black",
      size  = 3) +
      ggplot2::geom_point(
        ggplot2::aes(x = clean_pts[1:4, 2], y = clean_pts[1:4, 1]),
        col = "black",
        fill = "white",
        pch = 22
      ) +
      ggplot2::geom_point(ggplot2::aes(x = clean_pts[5:10, 2], y = clean_pts[5:10, 1]),
                          col = "gray50",
                          pch = 15) +
      ggplot2::geom_point(ggplot2::aes(x = clean_pts[5:10, 2], y = clean_pts[5:10, 1]),
                          col = "black",
                          pch = 0) +
      # Theme
      th +
      # Axis control
      ggplot2::scale_y_continuous(name = "x (m)", limits = c(-0.4, 0.01)) +
      ggplot2::scale_x_continuous(name = "y (m)",
                                  limits = c(0, 0.6),
                                  position = "top") +
      ggthemes::geom_rangeframe() +
      ggplot2::coord_fixed() +
      ggplot2::annotate(
        geom = "segment",
        x = log(0),
        xend = log(0),
        y = -0.4,
        yend = 0
      ) +
      ggplot2::annotate(
        geom = "segment",
        x = 0,
        xend = 0.6,
        y = -log(0),
        yend = -log(0)
      )

    if (plot_var == "yx") {
      plot(CGplot_x)
    }

    CGplot_z <- ggplot2::ggplot() +
      # Add in data
      ggplot2::geom_point(
        ggplot2::aes(x = prop_tertiary1$CG[2], y = -prop_tertiary1$CG[3]),
        col = "black",
        fill = "#BEA4BD",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(x = prop_tertiary2$CG[2], y = -prop_tertiary2$CG[3]),
        col = "black",
        fill = "#BEA4BD",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties_skin, object == "CGy")$value,
          y = -subset(mass_properties_skin, object == "CGz")$value
        ),
        col = "black",
        fill = "#BEA4BD",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties_bone, object == "CGy")$value,
          y = -subset(mass_properties_bone, object == "CGz")$value
        ),
        col = "black",
        fill = "#FAC5C6",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(primaries, object == "CGy")$value,
          y = -subset(primaries, object == "CGz")$value
        ),
        col = "black",
        fill = "#A0B3DC",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(secondaries, object == "CGy")$value,
          y = -subset(secondaries, object == "CGz")$value
        ),
        col = "black",
        fill = "#9AD09B",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties_muscle, object == "CGy")$value,
          y = -subset(mass_properties_muscle, object == "CGz")$value
        ),
        col = "black",
        fill = "#FAC5C6",
        pch = 21
      ) +
      ggplot2::geom_point(
        ggplot2::aes(
          x = subset(mass_properties, component == "wing" &
                       object == "CGy")$value,
          y = -subset(mass_properties, component == "wing" &
                        object == "CGz")$value
        ),
        col = "black",
        size  = 3
      ) +
      ggplot2::geom_point(
        ggplot2::aes(x = clean_pts[1:4, 2], y = -clean_pts[1:4, 3]),
        col = "black",
        fill = "white",
        pch = 22
      ) +
      ggplot2::geom_point(ggplot2::aes(x = clean_pts[5:10, 2], y = -clean_pts[5:10, 3]),
                          col = "gray50",
                          pch = 15) +
      ggplot2::geom_point(ggplot2::aes(x = clean_pts[5:10, 2], y = -clean_pts[5:10, 3]),
                          col = "black",
                          pch = 0) +
      # Theme
      th +
      # Axis control
      ggplot2::scale_y_continuous(name = "z (m)", limits = c(-0.2, 0.2)) +
      ggplot2::scale_x_continuous(
        name = "y (m)",
        limits = c(0, 0.6),
        position = "top"
      ) +
      ggthemes::geom_rangeframe() +
      ggplot2::coord_fixed() +
      ggplot2::annotate(
        geom = "segment",
        x = log(0),
        xend = log(0),
        y = -0.2,
        yend = 0.2
      ) +
      ggplot2::annotate(
        geom = "segment",
        x = 0,
        xend = 0.6,
        y = -log(0),
        yend = -log(0)
      )

    if (plot_var == "yz") {
      plot(CGplot_z)
    }

    return(CGplot_x)
  }