section_plot: Make an oceanographic section plot from an x-y-z data frame
In MikkoVihtakari/WaterMass: Helpers for the Analysis of Oceanographic Data

Description Usage Arguments Details Value Author(s) Examples

Creates an oceanographic section plot from a data frame using ggplot2. Returns either an interpolated section or a bubble plot.

section_plot(
  df,
  x,
  y,
  z,
  bottom = NULL,
  interpolate = FALSE,
  interp_method = "mba",
  log_y = FALSE,
  xlab = "Distance",
  ylab = "Depth",
  zlab = "Variable",
  ybreaks = waiver(),
  xbreaks = waiver(),
  zbreaks = waiver(),
  contour = NULL,
  contour_label_cex = 0.8,
  contour_color = "white",
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  zscale = "viridis",
  zcolor = "black",
  add_bottom = NULL,
  sampling_indicator = "lines",
  legend.position = "right",
  base_size = 10,
  ...
)

`df`	Data frame containing the data
`x`	Character specifying the column name which should be used as x (=distance) axis
`y`	Character specifying the column name which should be used as y (=depth) axis. The y axis will be inverted in the resulting plot.
`z`	Character specifying the column name which should be for bubbles or interpolation fill depending on the `interpolate` argument.
`bottom`	Optional character specifying the column name which contains bottom depths OR a data frame with x-axis values in the first column and bottom depths in the second column. If provided, unique combinations of `x` and `bottom` will be used to plot bottom for the section plot
`interpolate`	Logical indicating whether an interpolated section plot (`TRUE`) or a bubble plot (`FALSE`) should be returned.
`interp_method`	(`interpolate = TRUE` only). Character specifying the interpolation method. See `interpolate_section`.
`log_y`	logical indicating whether the y-axis should be `log10(y + 10)` transformed before plotting. Helps showing differences close to the surface if some stations are much deeper than others.
`xlab, ylab, zlab`	Character specifying the labels for the x-axis, y-axis and legend, respectively.
`xbreaks, ybreaks, zbreaks`	Numeric vector specifying the breaks for the x-axis, y-axis and legend. See scale_continuous.
`contour`	(`interpolate = TRUE` only). Numeric vector defining breaks for contour lines. Use `NULL` not to plot the contour lines.
`contour_label_cex`	Numeric giving the `cex` (=size) parameter for contour labels. See `geom_dl`.
`contour_color`	Character defining the color to be used for contour lines and labels.
`xlim, ylim`	Numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum. Use `NULL` for default limits.
`zlim`	Numeric vector of length two providing limits for fill or bubble size. Any values outside these limits will get the extreme values defined by `zrange` (using the `squish` function).
`zscale`	(`interpolate = TRUE` only). Character specifying the color scale for interpolation tile fill. Either one of the `scale_colour_viridis_c` `option` alternatives ("A", "B", "C", or "D") or "gradient2" for a `scale_colour_gradient2` (red-white-blue) color scale. Note that you can use the ggplot2 color scale arguments to adjust the color scales as you want. Just place them inside the `section_plot` function.
`zcolor`	(`interpolate = FALSE` only). Character specifying the color of bubbles. Use column name in `df` to scale a variable to bubble color (not implemented yet, here as a reminder).
`add_bottom`	Numeric vector of length two providing the depths that should be added to `bottom` at the extremes (`range`) of `xbreaks`. Useful for extending the plot giving space for graphical elements.
`sampling_indicator`	(`interpolate = TRUE` only). Character giving the style of sampling indicator. Alternatives: `"lines"` A dashed line reaching from data start depth to end depth at each station. Recommended for CTD sections. `"points"` Points indicating the vertical and horizontal location of sample. Recommended for water samples. `"ticks"` A black tick mark above the plot indicating the horizontal location of each station. A way to avoid clutter. `"none"` No sampling indicator will be plotted.
`legend.position`	Position for the ggplot legend. See the argument with the same name in theme.
`base_size`	Base size parameter for ggplot. See theme_bw.
`...`	Additional arguments passed to color and size scales. See `scale_colour_gradient2`, `scale_colour_viridis_c` and `scale_size`.

Note that you can use the ggplot2 color and size scale arguments to adjust the scales as you want. Just place them inside the section_plot function. See scale_colour_gradient2, scale_colour_viridis_c and scale_size.

Returns either an interpolated section (geom_tile) or a bubble (geom_point) ggplot2 object.

Mikko Vihtakari

# Bubble plots
section_plot(df = chlorophyll[grepl("KpN.|Kb[0-4]", chlorophyll$Station),], x = "lon", y = "From",
  z = "Chla")

# Interpolated CTD sections
## Standard temperature section plot. Difficult to see surface due to large differences in y-scale
section_plot(ctd_rijpfjord, x = "dist", y = "pressure", z = "temp", bottom = "bdepth",
interpolate = TRUE)

## Logarithmic y axis
section_plot(ctd_rijpfjord, x = "dist", y = "pressure", z = "temp", bottom = "bdepth",
interpolate = TRUE, log_y = TRUE)

## Contour lines
section_plot(ctd_rijpfjord, x = "dist", y = "pressure", z = "temp", bottom = "bdepth",
interpolate = TRUE, log_y = TRUE, contour = c(-1.8, 0, 1, 3))

## Duplicate values are averaged

df <- data.frame(X = rep(1:5, each = 3), Y = 1:3, Z = c(rep(0, 7), 2, rep(0, 7)))
section_plot(df, x = "X", y = "Y", z = "Z", interpolate = TRUE)

### Compare to:
section_plot(rbind(df, data.frame(X = 3, Y = 2, Z = 0)),
            x = "X", y = "Y", z = "Z", interpolate = TRUE)