R: Plot Echosounder Data

plot,echosounder-method {oce} | R Documentation

## Plot Echosounder Data

### 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] + 1, mgp[1] + 1, mgp[1] + 1, mgp[1] + 1), atTop,
      labelsTop, tformat, debug = getOption("oceDebug"), ...)

### Arguments

`x` | An `echosounder` object, e.g. as read by `read.echosounder`, or created by `as.echosounder`.
`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

    ## Not run:
    library(oce)
    data(echosounder)
    plot(echosounder, which=c(1,2), drawBottom=TRUE)

    ## End(Not run)

[Package oce version 1.0-1 Index]