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 specifie 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 = oce.colorsJet, lwd = 2,
      despike = FALSE, drawBottom, ignore = 5, drawTimeRange = FALSE,
      drawPalette = TRUE, radius, coastline, adorn = NULL,
      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 colour scale.
`type` | type of graph, `"l"` for line, `"p"` for points, or `"b"` for both.
`col` | colour 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 colour, then that colour 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"`.
`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.)
`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 0.9-20 Index]