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 colours (`col.salinity`, etc.) are ony used if two profiles appear on a plot.

### Usage

    plotProfile(x, xtype = "salinity+temperature", ytype = c("pressure", "z",
      "depth", "sigmaTheta"), 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, 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"), ...)

### Arguments

`x` | A `ctd` object, i.e. one inheriting from `ctd-class`.
`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. list("salinity") Profile of salinity. list("conductivity") Profile of conductivity. list("temperature") Profile of in-situ temperature. list("theta") Profile of potential temperature. list("density") Profile of density (expressed as sigma_theta). list("index") Index of sample (very useful for working with `ctdTrim`). list("salinity+temperature") Profile of salinity and temperature within a single axis frame. list("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. list("density+N2") Profile of sigma-theta and the square of buoyancy frequency within a single axis frame. list("density+dpdt") Profile of sigma-theta 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. list("spice") Profile of spice list("Rrho") Profile of Rrho, defined in the diffusive sense list("RrhoSF") Profile of Rrho, defined in the salt-finger sense an expression an expression to be evaluated, in the calling environment, for some quantity; in this case, it makes sense to specify also `xlab`.
`ytype` | variable to use on y axis; note that `z` is the negative of `depth`.
`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).
`ylab` | optional label for y axis. Set to `""` to prevent labelling the axis.
`col` | colour for a general profile.
`col.salinity` | colour for salinity profile (see “Details”).
`col.temperature` | colour for temperature (see “Details”).
`col.rho` | colour for density (see “Details”).
`col.N2` | colour for square of buoyancy frequency (see “Details”).
`col.dpdt` | colour for dP/dt.
`col.time` | colour for delta-time.
`pt.bg` | inside colour for symbols with `pch` in 21:25
`grid` | logical, set to `TRUE` to get a grid.
`col.grid` | colour 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`.
`ylim` | Optional limit for y axis, which can apply to any plot type, although is overridden by `plim` if `ytype=="pressure"`.
`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,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`, `plotScan`, `plotTS`, `tidem-class`

Other things related to `ctd` data: `[[,ctd-method`, `[[<-,ctd-method`, `as.ctd`, `cnvName2oceName`, `ctd-class`, `ctdDecimate`, `ctdFindProfiles`, `ctdRaw`, `ctdTrim`, `ctd`, `handleFlags,ctd-method`, `plot,ctd-method`, `plotScan`, `plotTS`, `read.ctd.itp`, `read.ctd.odf`, `read.ctd.sbe`, `read.ctd.woce.other`, `read.ctd.woce`, `read.ctd`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames`, `write.ctd`

### Examples

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

[Package oce version 0.9-20 Index]