R: Plot ADP Data

plot,adp-method {oce} | R Documentation

## Plot ADP Data

### Description

Create a summary plot of data measured by an acoustic doppler profiler.

### Usage

    ## S4 method for signature 'adp'
    plot(x, which = 1:dim(x@data$v)[3], mode = c("normal",
      "diagnostic"), col, breaks, zlim, titles, lwd = par("lwd"), type = "l",
      ytype = c("profile", "distance"), adorn = NULL,
      drawTimeRange = getOption("oceDrawTimeRange"), useSmoothScatter,
      missingColor = "gray", mgp = getOption("oceMgp"), mar = c(mgp[1] + 1.5,
      mgp[1] + 1.5, 1.5, 1.5), mai.palette = rep(0, 4), tformat,
      marginsAsImage = FALSE, cex = par("cex"), cex.axis = par("cex.axis"),
      cex.main = par("cex.main"), xlim, ylim, control, useLayout = FALSE,
      coastline = "coastlineWorld", span = 300, main = "", grid = FALSE,
      grid.col = "darkgray", grid.lty = "dotted", grid.lwd = 1,
      debug = getOption("oceDebug"), ...)

### Arguments

`x` | An `adp` object, i.e. one inheriting from `adp-class`.
`which` | list of desired plot types. These are graphed in panels running down from the top of the page. See “Details” for the meanings of various values of `which`.
`mode` | a string indicating whether to plot the conventional signal (`normal`) or or, in the special case of Aquadopp single-bin profilers, possibly the `diagnostic` signal. This argument is ignored except in the case of Aquadopp instruments. Perhaps a third option will become available in the future, for the `burst` mode that some instruments provide.
`col` | optional indication of colour(s) to use. If not provided, the default for images is `oce.colorsPalette(128,1)`, and for lines and points is black.
`breaks` | optional breaks for colour scheme
`zlim` | a range to be used as the `zlim` parameter to the `imagep` call that is used to create the image. If omitted, `zlim` is set for each panel individually, to encompass the data of the panel and to be centred around zero. If provided as a two-element vector, then that is used for each panel. If provided as a two-column matrix, then each panel of the graph uses the corresponding row of the matrix; for example, setting `zlim=rbind(c(-1,1),c(-1,1),c(-.1,.1))` might make sense for `which=1:3`, so that the two horizontal velocities have one scale, and the smaller vertical velocity has another.
`titles` | optional vector of character strings to be used as labels for the plot panels. For images, these strings will be placed in the right hand side of the top margin. For timeseries, these strings are ignored. If this is provided, its length must equal that of `which`.
`lwd` | if the plot is of a time-series or scattergraph format with lines, this is used in the usual way; otherwise, e.g. for image formats, this is ignored.
`type` | if the plot is of a time-series or scattergraph format, this is used in the usual way, e.g. `"l"` for lines, etc.; otherwise, as for image formats, this is ignored.
`ytype` | character string controlling the type of the y axis for images (ignored for time series). If `"distance"`, then the y axis will be distance from the sensor head, with smaller distances nearer the bottom of the graph. If `"profile"`, then this will still be true for upward-looking instruments, but the y axis will be flipped for downward-looking instruments, so that in either case, the top of the graph will represent the sample nearest the sea surface.
`adorn` | (Defunct) An `expression` or vector of expressions that contain R code that is to be executed immediately after each panel of the plot. If the number of expressions matches the number of panels, then the expressions are used for the corresponding panels; otherwise, the expression list is extended to match the number of panels (i.e. to obtain `length(which)` elements). Note that `adorn` is a dangerous argument, because if the expressions contained therein set up local storage, there is a chance of entirely disrupting the plotting. For this reason, `adorn` was marked as defunct in June 2016, and will be removed entirely after the July CRAN release. Users with existing code that uses `adorn` should simply plot the panels individually, and use conventional R functions, e.g. `lines` etc., after each panel, to achieve the desired effect. (See `oce-defunct` for notes on other deprecated or defunct `oce` features.)
`drawTimeRange` | boolean that applies to panels with time as the horizontal axis, indicating whether to draw the time range in the top-left margin of the plot.
`useSmoothScatter` | boolean that indicates whether to use `smoothScatter` in various plots, such as `which="uv"`. If not provided a default is used, with `smoothScatter` being used if there are more than 2000 points to plot.
`missingColor` | colour used to indicate `NA` values in images (see `imagep`); set to `NULL` to avoid this indication.
`mgp` | A three-element numerical vector to use for `par(mgp)` to control spacing of axis elements. The default is tighter than the R default, in order to use more space for the data and less for the axes.
`mar` | A four-element numerical vector to be used with `par("mar")`.
`mai.palette` | margins, in inches, to be added to those calculated for the palette; alter from the default only with caution
`tformat` | optional argument passed to `oce.plot.ts`, for plot types that call that function. (See `strptime` for the format used.)
`marginsAsImage` | boolean, `TRUE` to put a wide margin to the right of time-series plots, even if there are no images in the `which` list. (The margin is made wide if there are some images in the sequence.)
`cex` | size of labels on axes; see `par`("cex").
`cex.axis` | see `par`("cex.axis").
`cex.main` | see `par`("cex.main").
`xlim` | optional 2-element list for `xlim`, or 2-column matrix, in which case the rows are used, in order, for the panels of the graph.
`ylim` | optional 2-element list for `ylim`, or 2-column matrix, in which case the rows are used, in order, for the panels of the graph.
`control` | optional list of parameters that may be used for different plot types. Possibilities are `drawBottom` (a boolean that indicates whether to draw the bottom) and `bin` (a numeric giving the index of the bin on which to act, as explained in “Details”).
`useLayout` | set to `FALSE` to prevent using `layout` to set up the plot. This is needed if the call is to be part of a sequence set up by e.g. `par(mfrow)`.
`coastline` | a `coastline` object, or a character string naming one. This is used only for `which="map"`. See notes at `plot,ctd-method` for more information on built-in coastlines.
`span` | approximate span of map in km
`main` | main title for plot, used just on the top panel, if there are several panels.
`grid` | if `TRUE`, a grid will be drawn for each panel. (This argument is needed, because calling `grid` after doing a sequence of plots will not result in useful results for the individual panels.
`grid.col` | colour of grid
`grid.lty` | line type of grid
`grid.lwd` | line width of grid
`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. For example, supplying `despike=TRUE` will cause time-series panels to be de-spiked with `despike`. Another common action is to set the colour for missing values on image plots, with the argument `missingColor` (see `imagep`). Note that it is an error to give `breaks` in ..., if the formal argument `zlim` was also given, because they could contradict each other.

### Details

The plot may have one or more panels, with the content being controlled by the `which` argument.

- `which=1:4` (or `which="u1"` to `"u4"`) yield a distance-time image plot of a velocity component. If `x` is in `beam` coordinates (signalled by `metadata$oce.coordinate=="beam"`), this will be the beam velocity, labelled `b[1]` etc. If `x` is in xyz coordinates (sometimes called frame coordinates, or ship coordinates), it will be the velocity component to the right of the frame or ship (labelled `u` etc). Finally, if `x` is in `"enu"` coordinates, the image will show the the eastward component (labelled `east`). If `x` is in `"other"` coordinates, it will be component corresponding to east, after rotation (labelled `u\'`). Note that the coordinate is set by `read.adp`, or by `beamToXyzAdp`, `xyzToEnuAdp`, or `enuToOtherAdp`.

- `which=5:8` (or `which="a1"` to `"a4"`) yield distance-time images of backscatter intensity of the respective beams. (For data derived from Teledyn-RDI instruments, this is the item called “echo intensity.”)

- `which=9:12` (or `which="q1"` to `"q4"`) yield distance-time images of signal quality for the respective beams. (For RDI data derived from instruments, this is the item called “correlation magnitude.”)

- `which=60` or `which="map"` draw a map of location(s).

- `which=70:73` (or `which="g1"` to `"g4"`) yield distance-time images of percent-good for the respective beams. (For data derived from Teledyne-RDI instruments, which are the only instruments that yield this item, it is called “percent good.”)

- `which=80:83` (or `which="vv"`, `which="va"`, `which="vq"`, and `which="vg"`) yield distance-time images of the vertical beam fields for a 5 beam "SentinelV" ADCP from Teledyne RDI.

- `which="vertical"` yields a two panel distance-time image of vertical beam velocity and amplitude.

- `which=13` (or `which="salinity"`) yields a time-series plot of salinity.

- `which=14` (or `which="temperature"`) yields a time-series plot of temperature.

- `which=15` (or `which="pressure"`) yields a time-series plot of pressure.

- `which=16` (or `which="heading"`) yields a time-series plot of instrument heading.

- `which=17` (or `which="pitch"`) yields a time-series plot of instrument pitch.

- `which=18` (or `which="roll"`) yields a time-series plot of instrument roll.

- `which=19` yields a time-series plot of distance-averaged velocity for beam 1, rightward velocity, eastward velocity, or rotated-eastward velocity, depending on the coordinate system.

- `which=20` yields a time-series of distance-averaged velocity for beam 2, foreward velocity, northward velocity, or rotated-northward velocity, depending on the coordinate system.

- `which=21` yields a time-series of distance-averaged velocity for beam 3, up-frame velocity, upward velocity, or rotated-upward velocity, depending on the coordinate system.

- `which=22` yields a time-series of distance-averaged velocity for beam 4, for `beam` coordinates, or velocity estimate, for other coordinates. (This is ignored for 3-beam data.)

- `which=23` yields a progressive-vector diagram in the horizontal plane, plotted with `asp=1`. Normally, the depth-averaged velocity components are used, but if the `control` list contains an item named `bin`, then the depth bin will be used (with an error resulting if the bin is out of range).

- `which=24` yields a time-averaged profile of the first component of velocity (see `which=19` for the meaning of the component, in various coordinate systems).

- `which=25` as for 24, but the second component.

- `which=26` as for 24, but the third component.

- `which=27` as for 24, but the fourth component (if that makes sense, for the given instrument).

- `which=28` or `"uv"` yields velocity plot in the horizontal plane, i.e. u[2] versus u[1]. If the number of data points is small, a scattergraph is used, but if it is large, `smoothScatter` is used.

- `which=29` or `"uv+ellipse"` as the `"uv"` case, but with an added indication of the tidal ellipse, calculated from the eigen vectors of the covariance matrix.

- `which=30` or `"uv+ellipse+arrow"` as the `"uv+ellipse"` case, but with an added arrow indicating the mean current.

- `which=40` or `"bottomRange"` for average bottom range from all beams of the instrument.

- `which=41` to `44` (or `"bottomRange1"` to `"bottomRange4"`) for bottom range from beams 1 to 4.

- `which=50` or `"bottomVelocity"` for average bottom velocity from all beams of the instrument.

- `which=51` to `54` (or `"bottomVelocity1"` to `"bottomVelocity4"`) for bottom velocity from beams 1 to 4.

- `which=55` (or `"heaving"`) for time-integrated, depth-averaged, vertical velocity, i.e. a time series of heaving.

- `which=100` (or `"soundSpeed"`) for a time series of sound speed.

In addition to the above, there are some groupings defined:

- `which="velocity"` equivalent to `which=1:3` (velocity components)

- `which="amplitude"` equivalent to `which=5:7` (backscatter intensity components)

- `which="quality"` equivalent to `which=9:11` (quality components)

- `which="hydrography"` equivalent to `which=14:15` (temperature and pressure)

- `which="angles"` equivalent to `which=16:18` (heading, pitch and roll)

The colour scheme for image plots (`which` in 1:12) is provided by the `col` argument, which is passed to `image` to do the actual plotting. See “Examples” for some comparisons.

A common quick-look plot to assess mooring movement is to use `which=15:18` (pressure being included to signal the tide, and tidal currents may dislodge a mooring or cause it to settle).

By default, `plot,adp-method` uses a `zlim` value for the `image` that is constructed to contain all the data, but to be symmetric about zero. This is done on a per-panel basis, and the scale is plotted at the top-right corner, along with the name of the variable being plotted. You may also supply `zlim` as one of the ... arguments, but be aware that a reasonable limit on horizontal velocity components is unlikely to be of much use for the vertical component.

A good first step in the analysis of measurements made from a moored device (stored in `d`, say) is to do `plot(d, which=14:18)`. This shows time series of water properties and sensor orientation, which is helpful in deciding which data to trim at the start and end of the deployment, because they were measured on the dock or on the ship as it travelled to the mooring site.

### 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

### See Also

Other functions that plot `oce` data: `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`, `plotProfile`, `plotScan`, `plotTS`, `tidem-class`

Other things related to `adp` data: `[[,adp-method`, `[[<-,adp-method`, `adp-class`, `adp`, `as.adp`, `beamName`, `beamToXyzAdp`, `beamToXyzAdv`, `beamToXyz`, `beamUnspreadAdp`, `binmapAdp`, `enuToOtherAdp`, `enuToOther`, `read.adp.nortek`, `read.adp.rdi`, `read.adp.sontek.serial`, `read.adp.sontek`, `read.adp`, `read.aquadoppHR`, `read.aquadoppProfiler`, `read.aquadopp`, `subset,adp-method`, `summary,adp-method`, `toEnuAdp`, `toEnu`, `velocityStatistics`, `xyzToEnuAdp`, `xyzToEnu`

### Examples

    library(oce)
    data(adp)
    plot(adp, which=1:3)
    plot(adp, which='temperature', tformat='%H:%M')

[Package oce version 0.9-20 Index]