R: Add layers to a lattice plot, optionally using a new data...

layer {latticeExtra} | R Documentation

## Add layers to a lattice plot, optionally using a new data source

### Description

A mechanism to add new layers to a trellis object, optionally using a new data source. This is an alternative to modifying the panel function. Note the non-standard evaluation in `layer()`.

### Usage

    layer(..., data, magicdots, exclude,
          packets, rows, columns, groups,
          style, force, theme, under, superpose)

    layer_(...)
    glayer(...)
    glayer_(...)

    ## S3 method for class 'trellis'
    object + lay

    drawLayer(lay, panelArgs = trellis.panelArgs())

    flattenPanel(object)

### Arguments

`...` | expressions as they would appear in a panel function. These can refer to the panel function arguments (such as `x`, `y` and `subscripts`), and also to any named objects passed in through the `data` argument. The calls can also include the special argument “`...`”; in the default case of `magicdots = TRUE`, only those arguments which are not already named in a call are passed on through “`...`”. Otherwise, “`...`” simply represents all panel function arguments. See Details, below.
`data` | optional. A named `list` containing objects needed when evaluating (drawing) the layer.
`magicdots, exclude` | if `magicdots = TRUE`, the default, any reference to “`...`” in the layer expressions will only pass on those arguments from the panel function which are not named in the call (thus avoiding duplicate argument errors). If the first argument in a call is not named, it is assumed to be named `"x"`, and if the second argument is not named it is assumed to be named `"y"`. Furthermore, any argument names given in `exclude` will not be passed on through “`...`”.
`packets, rows, columns, groups` | restricts the layer to draw only in specified packets (which refer to individual panels, but are independent of their layout), or rows or columns of the trellis layout (`trellis.currentLayout`). For group layers (using `glayer` or `superpose = TRUE`), the groups can be restricted also, by specifying group numbers (or group values, as character strings). Negative values exclude the given items.
`style` | style index of the layer, used only to set lattice graphical parameters (same effect as in grouped displays). Note that this will use the theme settings in effect in the existing plot, which may or may not be what is desired. It may be necessary to use `force = TRUE` to escape from the plot's settings and use the current theme.
`force` | `force = TRUE` is just a shorthand for `theme = trellis.par.get()`, which is useful for over-riding the theme settings in effect in an existing plot. For instance, if the original plot specified `par.settings = simpleTheme(col = "red")` then the theme settings in effect will be entirely red. Use `force = TRUE` to reset the current theme for this layer, or use `theme` directly.
`theme` | a style specification to be passed to `trellis.par.set` which has effect only while drawing the layer. One can pass a whole theme specification list, such as `theme = custom.theme()`, or a more specific list, such as `theme = simpleTheme(col = "red")`.
`under` | whether the layer should be drawn before the existing panel function. This defaults to `TRUE` in the convenience functions `layer_()` and `glayer_()`.
`superpose` | if `TRUE`, the layer will be drawn once for each level of any `groups` in the plot, using `panel.superpose`. This defaults to `TRUE` in the convenience functions `glayer()` and `glayer_()`.
`object` | a trellis object.
`lay` | a layer object.
`panelArgs` | list of arguments to the panel function.

### Details

The `layer` mechanism is a method for augmenting a panel function. It allows expressions to be added to the panel function without knowing what the original panel function was. In this way it can be useful for convenient augmentation of trellis plots.

Note that the evaluation used in `layer` is non-standard, and can be confusing at first: you typically refer to variables as if inside the panel function (`x`, `y`, etc); you can usually refer to objects which exist in the global environment (workspace), but it is safer to pass them in by name in the `data` argument to `layer`. (And this should not to be confused with the `data` argument to the original `xyplot`.)

A simple example is adding a reference line to each panel: `layer(panel.refline(h = 0))`. Note that the expressions are quoted, so if you have local variables they will need to be either accessible globally, or passed in via the `data` argument. For example:

`layer(panel.refline(h = myVal)) ## if myVal is global`

`layer(panel.refline(h = h), data = list(h = myVal))`

Another non-standard aspect is that the special argument “`...`” will, by default, only pass through those argument not already named. For example, this will over-ride the `x` argument and pass on the remaining arguments:

`layer(panel.xyplot(x = jitter(x), ...))`

The first un-named argument is assumed to be "x", so that is the same as

`layer(panel.xyplot(jitter(x), ...))`

The layer mechanism should probably still be considered experimental.

`drawLayer()` actually draws the given layer object, applying the panel specification, style settings and so on. It should only be called while a panel is in focus.

The `flattenPanel` function will construct a human-readable function incorporating code from all layers (and the original panel function). Note that this does not return a usable function, as it lacks the correct argument list and ignores any extra data sources that layers might use. It is intended be edited manually.

### Value

a `layer` object is defined as a list of expression objects, each of which may have a set of attributes. The result of "adding" a layer to a trellis object (`+.trellis`) is the updated trellis object.

### Author(s)

Felix Andrews felix@nfrac.org

### See Also

`update.trellis`, `as.layer` for overlaying entire plots

### Examples

    foo <- xyplot(ozone ~ wind, environmental)
    foo

    ## overlay reference lines
    foo <- foo + layer(panel.abline(h = 0)) +
                 layer(panel.lmline(x, y, lty = 2))

    ## underlay a flat color
    foo <- foo + layer(panel.fill(grey(.95)), under = TRUE)
    foo

    ## layers can access the panel function arguments
    foo <- foo + layer({ ok <- (y>100);
                panel.text(x[ok], y[ok], y[ok], pos = 1) })
    foo

    ## over-ride arguments by name
    foo <- foo +
      layer(panel.xyplot(y = ave(y, x, FUN = max), type = "a", ...))
    foo

    ## see a sketch of the complete panel function
    flattenPanel(foo)

    ## group layers, drawn for each group in each panel
    dotplot(VADeaths, type = "o") +
      glayer(ltext(x[5], y[5], group.value, srt = 40))

    ## a quick way to print out the panel.groups arguments:
    dotplot(VADeaths, type = "o") + glayer(str(list(...)))

    ## layers with superposed styles
    xyplot(ozone ~ wind | equal.count(temperature, 2),
           data = environmental) +
       layer(panel.loess(x, y, span = 0.5), style = 1) +
       layer(panel.loess(x, y, span = 1.0), style = 2) +
       layer(panel.key(c("span = 0.5", "span = 1.0"), corner = c(1,.98),
                       lines = TRUE, points = FALSE), packets = 1)

    ## note that styles come from the settings in effect in the plot,
    ## which is not always what you want:
    xyplot(1:10 ~ 1:10, type = "b", par.settings = simpleTheme(col = "red")) +
      layer(panel.lines(x = jitter(x, 2), ...)) +  ## drawn in red
      layer(panel.lines(x = jitter(x, 2), ...), force = TRUE)  ## reset theme

    ## using other variables from the original `data` object
    ## NOTE: need subscripts = TRUE in original call!
    zoip <- xyplot(wind ~ temperature | equal.count(radiation, 2),
       data = environmental, subscripts = TRUE)
    zoip + layer(panel.points(..., pch = 19,
                 col = grey(1 - ozone[subscripts] / max(ozone))),
           data = environmental)

    ## restrict drawing to specified panels
    barchart(yield ~ variety | site, data = barley,
             groups = year, layout = c(1,6), as.table = TRUE,
             scales = list(x = list(rot = 45))) +
    layer(ltext(tapply(y, x, max), lab = abbreviate(levels(x)),
          pos = 3), rows = 1)

    ## example of a new data source
    qua <- xyplot(lat ~ long | cut(depth, 2), quakes,
        aspect = "iso", pch = ".", cex = 2)
    qua
    ## add layer showing distance from Auckland
    newdat <- with(quakes, expand.grid(
                gridlat = seq(min(lat), max(lat), length = 60),
                gridlon = seq(min(long), max(long), length = 60)))
    newdat$dist <- with(newdat, sqrt((gridlat - -36.87)^2 +
                                     (gridlon - 174.75)^2))
    qua + layer_(panel.contourplot(x = gridlon, y = gridlat, z = dist,
       contour = TRUE, subscripts = TRUE), data = newdat)

[Package latticeExtra version 0.6-28 Index]