R: Plot an echosounder Object

plot,echosounder-method {oce} | R Documentation

## Plot an echosounder Object

### Description

Plot echosounder data. Simple linear approximation is used when a `newx` value is specified with the `which=2` method, but arguably a gridding method should be used, and this may be added in the future.

### Usage

    ## S4 method for signature 'echosounder'
    plot(
      x,
      which = 1,
      beam = "a",
      newx,
      xlab,
      ylab,
      xlim,
      ylim,
      zlim,
      type = "l",
      col = oceColorsJet,
      lwd = 2,
      despike = FALSE,
      drawBottom,
      ignore = 5,
      drawTimeRange = FALSE,
      drawPalette = TRUE,
      radius,
      coastline,
      mgp = getOption("oceMgp"),
      mar = c(mgp[1], mgp[1] + 1.5, mgp[2] + 1/2, 1/2),
      atTop,
      labelsTop,
      tformat,
      debug = getOption("oceDebug"),
      ...
    )

### Arguments

`x` | an echosounder object.
`which` | list of desired plot types: `which=1` or `which="zt image"` gives a z-time image, `which=2` or `which="zx image"` gives a z-distance image, and `which=3` or `which="map"` gives a map showing the cruise track. In the image plots, the display is of `log10()` of amplitude, trimmed to zero for any amplitude values less than 1 (including missing values, which equal 0). Add 10 to the numeric codes to get the secondary data (non-existent for single-beam files,
`beam` | a more detailed specification of the data to be plotted. For single-beam data, this may only be `"a"`. For dual-beam data, this may be `"a"` for the narrow-beam signal, or `"b"` for the wide-beam signal. For split-beam data, this may be `"a"` for amplitude, `"b"` for x-angle data, or `"c"` for y-angle data.
`newx` | optional vector of values to appear on the horizontal axis if `which=1`, instead of time. This must be of the same length as the time vector, because the image is remapped from time to `newx` using `approx()`.
`xlab, ylab` | optional labels for the horizontal and vertical axes; if not provided, the labels depend on the value of `which`.
`xlim` | optional range for x axis.
`ylim` | optional range for y axis.
`zlim` | optional range for color scale.
`type` | type of graph, `"l"` for line, `"p"` for points, or `"b"` for both.
`col` | color scale for image, a function
`lwd` | line width (ignored if `type="p"`)
`despike` | remove vertical banding by using `smooth()` to smooth across image columns, row by row.
`drawBottom` | optional flag used for section images. If `TRUE`, then the bottom is inferred as a smoothed version of the ridge of highest image value, and data below that are grayed out after the image is drawn. If `drawBottom` is a color, then that color is used, instead of white. The bottom is detected with `findBottom()`, using the `ignore` value described next.
`ignore` | optional flag specifying the thickness in metres of a surface region to be ignored during the bottom-detection process. This is ignored unless `drawBottom=TRUE`.
`drawTimeRange` | if `TRUE`, the time range will be drawn at the top. Ignored except for `which=2`, i.e. distance-depth plots.
`drawPalette` | if `TRUE`, the palette will be drawn.
`radius` | radius to use for maps; ignored unless `which=3` or `which="map"`.
`coastline` | coastline to use for maps; ignored unless `which=3` or `which="map"`.
`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")`.
`atTop` | optional vector of time values, for labels at the top of the plot produced with `which=2`. If `labelsTop` is provided, then it will hold the labels. If `labelsTop` is not provided, the labels will be constructed with the `format()` function, and these may be customized by supplying a `format` in the `...` arguments.
`labelsTop` | optional vector of character strings to be plotted above the `atTop` times. Ignored unless `atTop` was provided.
`tformat` | optional argument passed to `imagep()`, for plot types that call that function. (See `strptime()` for the format used.)
`debug` | set to an integer exceeding zero, to get debugging information during processing.
`...` | optional arguments passed to plotting functions. For example, for maps, it is possible to specify the radius of the view in kilometres, with `radius`.

### 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, with extensive help from Clark Richards

### See Also

Other things related to echosounder data: `[[,echosounder-method`, `[[<-,echosounder-method`, `as.echosounder()`, `echosounder-class`, `echosounder`, `findBottom()`, `read.echosounder()`, `subset,echosounder-method`, `summary,echosounder-method`

### Examples

    library(oce)
    data(echosounder)
    plot(echosounder, drawBottom=TRUE)

[Package oce version 1.7-2 Index]