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,
      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) plotted on the x axis, either a vector of length equal to that of `pressure` in the `data` slot, or a text code from the list below. `"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"` and `"sigmaTheta"`.
`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, the value of `xtype` is used for the label.
`ylab` | optional label for y axis. Set to `""` to prevent 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 S axis
`Clim` | Optional limit for conductivity axis
`Tlim` | Optional limit for T axis
`densitylim` | Optional limit for density axis
`N2lim` | Optional limit for N2 axis
`Rrholim` | Optional limit for Rrho axis
`dpdtlim` | Optional limit for dp/dt axis
`timelim` | Optional limit for delta-time axis
`plim` | Optional limit for 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` | lwd 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

### See Also

`read.ctd()` scans ctd information from a file, `plot,ctd-method()` is a general plotting function for `ctd` objects, and `plotTS()` plots a temperature-salinity diagrams.

Other functions that plot oce data: `plot,adp-method`, `plot,adv-method`, `plot,amsr-method`, `plot,argo-method`, `plot,bremen-method`, `plot,cm-method`, `plot,coastline-method`, `plot,ctd-method`, `plot,gps-method`, `plot,ladp-method`, `plot,landsat-method`, `plot,lisst-method`, `plot,lobo-method`, `plot,met-method`, `plot,odf-method`, `plot,rsk-method`, `plot,satellite-method`, `plot,sealevel-method`, `plot,section-method`, `plot,tidem-method`, `plot,topo-method`, `plot,windrose-method`, `plot,xbt-method`, `plotScan()`, `plotTS()`, `tidem-class`

Other things related to ctd data: `CTD_BCD2014666_008_1_DN.ODF.gz`, `[[,ctd-method`, `[[<-,ctd-method`, `as.ctd()`, `cnvName2oceName()`, `ctd-class`, `ctd.cnv`, `ctdDecimate()`, `ctdFindProfiles()`, `ctdRaw`, `ctdTrim()`, `ctd`, `d200321-001.ctd`, `d201211_0011.cnv`, `handleFlags,ctd-method`, `initialize,ctd-method`, `initializeFlagScheme,ctd-method`, `oceNames2whpNames()`, `oceUnits2whpUnits()`, `plot,ctd-method`, `plotScan()`, `plotTS()`, `read.ctd.itp()`, `read.ctd.odf()`, `read.ctd.sbe()`, `read.ctd.woce.other()`, `read.ctd.woce()`, `read.ctd()`, `setFlags,ctd-method`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames()`, `woceUnit2oceUnit()`, `write.ctd()`

### Examples

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

[Package oce version 1.2-0 Index]