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

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().

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

Felix Andrews felix@nfrac.org

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)
#> {
#>     panel.fill(grey(0.95))
#>     panel.xyplot(...)
#>     panel.abline(h = 0)
#>     panel.lmline(x, y, lty = 2)
#>     {
#>         ok <- (y > 100)
#>         panel.text(x[ok], y[ok], y[ok], pos = 1)
#>     }
#>     do.call(panel.xyplot, modifyList(list(...), list(y = ave(y, 
#>         x, FUN = max), type = "a")))
#> }


## 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(...)))

#> List of 21
#>  $ x           : num [1:5] 11.7 18.1 26.9 41 66
#>  $ subscripts  : int [1:5] 1 2 3 4 5
#>  $ pch         : num 1
#>  $ cex         : num 0.8
#>  $ font        : num 1
#>  $ fontface    : NULL
#>  $ fontfamily  : NULL
#>  $ col         : chr "black"
#>  $ col.line    : chr "#0072B2"
#>  $ col.symbol  : chr "#0072B2"
#>  $ fill        : chr "#CCFFFF"
#>  $ lty         : num 1
#>  $ lwd         : num 1
#>  $ alpha       : num 1
#>  $ type        : chr "o"
#>  $ group.number: int 1
#>  $ group.value : chr "Rural Male"
#>  $ grid        : logi FALSE
#>  $ box.ratio   : num 1
#>  $ horizontal  : logi TRUE
#>  $ y           : num [1:5] 1 2 3 4 5
#> List of 21
#>  $ x           : num [1:5] 8.7 11.7 20.3 30.9 54.3
#>  $ subscripts  : int [1:5] 6 7 8 9 10
#>  $ pch         : num 1
#>  $ cex         : num 0.8
#>  $ font        : num 1
#>  $ fontface    : NULL
#>  $ fontfamily  : NULL
#>  $ col         : chr "black"
#>  $ col.line    : chr "#E69F00"
#>  $ col.symbol  : chr "#E69F00"
#>  $ fill        : chr "#FFCCFF"
#>  $ lty         : num 1
#>  $ lwd         : num 1
#>  $ alpha       : num 1
#>  $ type        : chr "o"
#>  $ group.number: int 2
#>  $ group.value : chr "Rural Female"
#>  $ grid        : logi FALSE
#>  $ box.ratio   : num 1
#>  $ horizontal  : logi TRUE
#>  $ y           : num [1:5] 1 2 3 4 5
#> List of 21
#>  $ x           : num [1:5] 15.4 24.3 37 54.6 71.1
#>  $ subscripts  : int [1:5] 11 12 13 14 15
#>  $ pch         : num 1
#>  $ cex         : num 0.8
#>  $ font        : num 1
#>  $ fontface    : NULL
#>  $ fontfamily  : NULL
#>  $ col         : chr "black"
#>  $ col.line    : chr "#009E73"
#>  $ col.symbol  : chr "#009E73"
#>  $ fill        : chr "#CCFFCC"
#>  $ lty         : num 1
#>  $ lwd         : num 1
#>  $ alpha       : num 1
#>  $ type        : chr "o"
#>  $ group.number: int 3
#>  $ group.value : chr "Urban Male"
#>  $ grid        : logi FALSE
#>  $ box.ratio   : num 1
#>  $ horizontal  : logi TRUE
#>  $ y           : num [1:5] 1 2 3 4 5
#> List of 21
#>  $ x           : num [1:5] 8.4 13.6 19.3 35.1 50
#>  $ subscripts  : int [1:5] 16 17 18 19 20
#>  $ pch         : num 1
#>  $ cex         : num 0.8
#>  $ font        : num 1
#>  $ fontface    : NULL
#>  $ fontfamily  : NULL
#>  $ col         : chr "black"
#>  $ col.line    : chr "#D55E00"
#>  $ col.symbol  : chr "#D55E00"
#>  $ fill        : chr "#FFE5CC"
#>  $ lty         : num 1
#>  $ lwd         : num 1
#>  $ alpha       : num 1
#>  $ type        : chr "o"
#>  $ group.number: int 4
#>  $ group.value : chr "Urban Female"
#>  $ grid        : logi FALSE
#>  $ box.ratio   : num 1
#>  $ horizontal  : logi TRUE
#>  $ y           : num [1:5] 1 2 3 4 5


## 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)