R: Plot a ctd Profile

plotProfile {oce}

R Documentation

Plot a ctd Profile

Description

Plot a profile, showing variation of some quantity (or quantities) with pressure, using the oceanographic convention of putting lower pressures nearer the top of the plot. This works for any oce object that has a pressure column in its data slot. The colors (col.salinity, etc.) are only used if two profiles appear on a plot.

Usage

plotProfile(
  x,
  xtype = "salinity+temperature",
  ytype = "pressure",
  eos = getOption("oceEOS", default = "gsw"),
  lty = 1,
  xlab = NULL,
  ylab = NULL,
  col = "black",
  col.salinity = "darkgreen",
  col.temperature = "red",
  col.rho = "blue",
  col.N2 = "brown",
  col.dpdt = "darkgreen",
  col.time = "darkgreen",
  pt.bg = "transparent",
  grid = TRUE,
  col.grid = "lightgray",
  lty.grid = "dotted",
  Slim,
  Clim,
  Tlim,
  densitylim,
  sigmalim,
  N2lim,
  Rrholim,
  dpdtlim,
  timelim,
  plim,
  xlim,
  ylim,
  lwd = par("lwd"),
  xaxs = "r",
  yaxs = "r",
  cex = 1,
  pch = 1,
  useSmoothScatter = FALSE,
  df,
  keepNA = FALSE,
  type = "l",
  mgp = getOption("oceMgp"),
  mar,
  add = FALSE,
  inset = FALSE,
  debug = getOption("oceDebug", 0),
  ...
)

Arguments

`x`	a ctd object.
`xtype`	item(s) to be plotted on the x axis, either a character value taken from the following list, or a numeric vector of length matching the `pressure` field stored in `x`. (In the second case, as of version 1.7-11, a label is auto-constructed, unless the user supplied a character value for `xlab`.) `"salinity"` Profile of salinity. `"conductivity"` Profile of conductivity. `"temperature"` Profile of in-situ temperature. `"theta"` Profile of potential temperature. `"density"` Profile of density (expressed as `\sigma_\theta`). `"index"` Index of sample (useful for working with `ctdTrim()`). `"salinity+temperature"` Profile of salinity and temperature within a single axis frame. `"N2"` Profile of square of buoyancy frequency `N^2`, calculated with `swN2()` with an optional argument setting of `df=length(x[["pressure"]])/4` to do some smoothing. `"density+N2"` Profile of sigma0 and the square of buoyancy frequency within a single axis frame. `"density+dpdt"` Profile of sigma0 and dP/dt for the sensor. The latter is useful in indicating problems with the deployment. It is calculated by first differencing pressure and then using a smoothing spline on the result (to avoid grid-point wiggles that result because the SBE software only writes 3 decimal places in pressure). Note that dP/dt may be off by a scale factor; this should not be a problem if there is a `time` column in the `data` slot, or a `sample.rate` in the `metadata` slot. `"sigma0"`, `"sigma1"`, `"sigma2"`, `"sigma3"` and `"sigma4"` Profile of potential density referenced to 0dbar (i.e. the surface), 1000dbar, 2000dbar, 3000dbar, and 4000dbar. `"spice"` Profile of spice. `"Rrho"` Profile of Rrho, defined in the diffusive sense. `"RrhoSF"` Profile of Rrho, defined in the salt-finger sense.
`ytype`	variable to use on y axis. The valid choices are: `"pressure"` (the default), `"z"`, `"depth"`, `"sigmaTheta"` and `"sigma0"`.
`eos`	equation of state to be used, either `"unesco"` or `"gsw"`.
`lty`	line type for the profile.
`xlab`	optional label for x axis (at top of plot). If not provided, a label is inferred from the value of `xtype`. For the user-supplied case, bear in mind that the easy way to get units is to use an expression, e.g. `xlab=expression("Acceleration ["m/s^2"]")`.
`ylab`	optional label for y axis. See `xlab` for a note on units. Setting `ylab=""` prevents labelling the axis.
`col`	color for a general profile.
`col.salinity`	color for salinity profile (see “Details”).
`col.temperature`	color for temperature (see “Details”).
`col.rho`	color for density (see “Details”).
`col.N2`	color for square of buoyancy frequency (see “Details”).
`col.dpdt`	color for dP/dt.
`col.time`	color for delta-time.
`pt.bg`	inside color for symbols with `pch` in 21:25
`grid`	logical, set to `TRUE` to get a grid.
`col.grid`	color for grid.
`lty.grid`	line type for grid.
`Slim`	optional limit for the salinity axis, which can either represent Practical Salinity or Absolute Salinity.
`Clim`	optional limit for the conductivity axis.
`Tlim`	optional limit for the temperature axis, which can represent in-situ temperature, potential temperature, or Conservative Temperature.
`densitylim`	optional limit for density axis.
`sigmalim`	optional limit for the density-anomaly axis, which can represent `sigmaTheta`, `sigma0`, `sigma1`, `sigma2`, `sigma3` or `sigma4`.
`N2lim`	optional limit for the N2 axis.
`Rrholim`	optional limit for the density ratio axis.
`dpdtlim`	optional limit for the dp/dt axis.
`timelim`	optional limit for the delta-time axis.
`plim`	optional limit for the pressure axis, ignored unless `ytype=="pressure"`, in which case it takes precedence over `ylim`.
`xlim`	optional limit for x axis, which can apply to any plot type. This is ignored if the plotted x variable is something for which a limit may be specified with an argument, e.g. `xlim` is ignored for a salinity profile, because `Slim` ought to be given in such a case.
`ylim`	optional limit for y axis, which can apply to any plot type, although is overridden by `plim` if `ytype` is `"pressure"` or by `densitylim` if `ytype` is `"sigmaTheta"`.
`lwd`	line width value for data line
`xaxs`	value of `par()` `xaxs` to use
`yaxs`	value of `par()` `yaxs` to use
`cex`	size to be used for plot symbols (see `par()`)
`pch`	code for plotting symbol (see `par()`).
`useSmoothScatter`	boolean, set to `TRUE` to use `smoothScatter()` instead of `plot()` to draw the plot.
`df`	optional argument, passed to `swN2()` if provided, and if a plot using `N^2` is requested.
`keepNA`	FALSE
`type`	type of plot to draw, using the same scheme as `plot()`.
`mgp`	3-element numerical vector to use for par`(mgp)`, and also for par`(mar)`, computed from this. The default is tighter than the R default, in order to use more space for the data and less for the axes.
`mar`	Four-element numerical value to be used to set the plot margins, with a call to par`(mar)` prior to the plot. If this is not supplied, a reasonable default will be set up.
`add`	A logical value that controls whether to add to an existing plot. (It makes sense to use `add=TRUE` in the `panel` argument of a `coplot()`, for example.)
`inset`	A logical value indicating whether to draw an inset plot. Setting this to `TRUE` will prevent the present function from adjusting the margins, which is necessary because margin adjustment is the basis for the method used by `plotInset()`.
`debug`	a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.
`...`	optional arguments passed to other functions. A common example is to set `df`, for use in `swN2()` calculations.

Value

None.

Author(s)

Dan Kelley

Examples

library(oce)
data(ctd)
plotProfile(ctd, xtype = "temperature")

[Package oce version 1.8-2 Index]