R: Plot Temperature-Salinity Diagram

plotTS {oce} | R Documentation

## Plot Temperature-Salinity Diagram

### Description

Creates a temperature-salinity plot for a CTD cast, with labeled isopycnals.

### Usage

    plotTS(
      x,
      inSitu = FALSE,
      type = "p",
      referencePressure = 0,
      nlevels = 6,
      levels,
      grid = TRUE,
      col.grid = "lightgray",
      lty.grid = "dotted",
      rho1000 = FALSE,
      eos = getOption("oceEOS", default = "gsw"),
      cex = par("cex"),
      col = par("col"),
      pch = par("pch"),
      bg = "white",
      pt.bg = "transparent",
      col.rho = gray(0.5),
      cex.rho = 3/4 * par("cex"),
      rotate = TRUE,
      useSmoothScatter = FALSE,
      xlab,
      ylab,
      Slim,
      Tlim,
      drawFreezing = TRUE,
      trimIsopycnals = TRUE,
      mgp = getOption("oceMgp"),
      mar = c(mgp[1] + 1.5, mgp[1] + 1.5, mgp[1], mgp[1]),
      lwd = par("lwd"),
      lty = par("lty"),
      lwd.rho = par("lwd"),
      lty.rho = par("lty"),
      add = FALSE,
      inset = FALSE,
      debug = getOption("oceDebug"),
      ...
    )

### Arguments

`x` | a ctd, argo or section object, or a list containing solely ctd objects or argo objects.
`inSitu` | A boolean indicating whether to use in-situ temperature or (the default) potential temperature, calculated with reference pressure given by `referencePressure`. This is ignored if `eos="gsw"`, because those cases the y axis is necessarily the conservative formulation of temperature.
`type` | representation of data, `"p"` for points, `"l"` for connecting lines, or `"n"` for no indication.
`referencePressure` | reference pressure, to be used in calculating potential temperature, if `inSitu` is `FALSE`.
`nlevels` | Number of automatically-selected isopycnal levels (ignored if `levels` is supplied).
`levels` | Optional vector of desired isopycnal levels.
`grid` | a flag that can be set to `TRUE` to get a grid.
`col.grid` | color for grid.
`lty.grid` | line type for grid.
`rho1000` | if TRUE, label isopycnals as e.g. 1024; if FALSE, label as e.g. 24
`eos` | equation of state to be used, either `"unesco"` or `"gsw"`.
`cex` | character-expansion factor for symbols, as in par`("cex")`.
`col` | color for symbols.
`pch` | symbol type, as in par`("pch")`.
`bg` | optional color to be painted under plotting area, before plotting. (This is useful for cases in which `inset=TRUE`.)
`pt.bg` | inside color for symbols with `pch` in 21:25
`col.rho` | color for isopycnal lines and their labels.
`cex.rho` | size of the isopycnal labels.
`rotate` | if TRUE, labels in right-hand margin are written vertically
`useSmoothScatter` | if TRUE, use `smoothScatter()` to plot the points.
`xlab` | optional label for the x axis, with default "Salinity [PSU]".
`ylab` | optional label for the y axis, with default "Temperature [C]".
`Slim` | optional limits for salinity axis, otherwise inferred from visible data (i.e. the data that have finite values for both salinity and temperature).
`Tlim` | as `Slim`, but for temperature.
`drawFreezing` | logical indication of whether to draw a freezing-point line. This is based on zero pressure. If `eos="unesco"` then `swTFreeze()` is used to compute the curve, whereas if `eos="gsw"` then `gsw::gsw_CT_freezing()` is used; in each case, zero pressure is used.
`trimIsopycnals` | logical value (`TRUE` by default) that indicates whether to trim isopycnal curves to the region of temperature-salinity space for which density computations are considered to be valid in the context of the chosen `eos`; see “Details”.
`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` | value to be used with par`("mar")`. If set to `NULL`, then par`("mar")` is used. A good choice for a TS diagram with a palette to the right is `mar=par("mar")+c(0, 0, 0, 1))`.
`lwd` | line width of lines or symbols.
`lty` | line type of lines or symbols.
`lwd.rho` | line width for density curves.
`lty.rho` | line type for density curves.
`add` | a flag 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` | set to `TRUE` for use within `plotInset()`. The effect is to prevent the present function from adjusting 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 plotting functions.

### Details

The isopycnal curves (along which density is constant) are drawn with `drawIsopycnals()`, which also places labels in the margins showing density minus 1000 kg/m^3. If `trimIsopycnals` is `TRUE` (which is the default), these curves are trimmed to the region within which the results of density calculation in the chosen equation of state (`eos`) are considered to be reliable.

With `eos="unesco"` this region includes Practical Salinity from 0 to 42 and Potential Temperature from -2C to 40C, in accordance with Fofonoff and Millard (1983, page 23).

With `eos="gsw"` the lower limit of Absolute Salinity validity is taken as 0 g/kg, in accordance with both McDougall et al. (2003 section 3) and the TEOS-10/gsw Matlab code for the so-called "funnel" of validity. However, an appropriate upper limit on Absolute Salinity is not as clear. Here, the value 42 g/kg is chosen to match the "funnel" Matlab code as of July 2020, but two other choices might have been made. One is 50 g/kg, since `gsw::gsw_SA_from_rho()` returns `NA` values for Absolute Salinities exceeding that value, and another is 40 g/kg, as in McDougall et al. (2003 section 3). The Conservative Temperature range is set to run from -2C to 33C, as in McDougall et al. (2003 section 3), even though the "funnel" imposes no upper limit on this variable.

### Value

A list is silently returned, containing `xat` and `yat`, values that can be used by `oce.grid()` to add a grid to the plot.

### Author(s)

Dan Kelley

### References

- Fofonoff, N. P., and R. C. Millard. "Algorithms for Computation of Fundamental Properties of Seawater." UNESCO Technical Papers in Marine Research. SCOR working group on Evaluation of CTD data; UNESCO/ICES/SCOR/IAPSO Joint Panel on Oceanographic Tables and Standards, 1983. https://unesdoc.unesco.org/ark:/48223/pf0000059832.

- McDougall, Trevor J., David R. Jackett, Daniel G. Wright, and Rainer Feistel. "Accurate and Computationally Efficient Algorithms for Potential Temperature and Density of Seawater." Journal of Atmospheric and Oceanic Technology 20, no. 5 (May 1, 2003): 730-41. `https://journals.ametsoc.org/jtech/article/20/5/730/2543/Accurate-and-Computationally-Efficient-Algorithms`.

### See Also

`summary,ctd-method()` summarizes the information, while `read.ctd()` scans it from a file.

Other functions that plot oce data: `download.amsr()`, `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`, `plotProfile()`, `plotScan()`, `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`, `ctdRepair()`, `ctdTrim()`, `ctd_aml.csv`, `ctd`, `d200321-001.ctd`, `d201211_0011.cnv`, `handleFlags,ctd-method`, `initialize,ctd-method`, `initializeFlagScheme,ctd-method`, `oceNames2whpNames()`, `oceUnits2whpUnits()`, `plot,ctd-method`, `plotProfile()`, `plotScan()`, `read.ctd.itp()`, `read.ctd.odf()`, `read.ctd.odv()`, `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

    ## For a simple ctd object
    library(oce)
    data(ctd)
    plotTS(ctd)

    ## For a section object (note the outlier!)
    data(section)
    plotTS(section)

    ## Adding a colormap based on a different variable, e.g. oxygen
    marOrig <- par("mar") # so later plots with palettes have same margins
    cm <- colormap(section[['oxygen']])
    drawPalette(colormap=cm, zlab='Oxygen')
    plotTS(section, pch=19, col=cm$zcol, mar=par('mar')) # the mar adjusts for the palette

    ## Coloring based on station:
    Tlim <- range(section[['temperature']], na.rm=TRUE)
    Slim <- range(section[['salinity']], na.rm=TRUE)
    cm <- colormap(seq_along(section[['latitude', 'byStation']]))
    par(mar=marOrig) # same as previous plot
    drawPalette(colormap=cm, zlab='Latitude')
    plotTS(section, Tlim=Tlim, Slim=Slim, pch=NA, mar=par('mar'))
    jnk <- mapply(
        function(s, col) {
            plotTS(s, col=col, add=TRUE, type='l')
        },
        section[['station']], col=cm$zcol)

    ## Show TS for an argo object
    data(argo)
    plotTS(handleFlags(argo))

[Package oce version 1.7-2 Index]