[R] Custom axis function in lattice:::xyplot

[Deepayan Sarkar]

On Wed, May 26, 2010 at 10:20 AM, Peter Ehlers <ehlers at ucalgary.ca> wrote:
> On 2010-05-26 4:03, Gavin Simpson wrote:
>>
>> Dear List,
>>
>> I have been writing a Lattice function to draw what we call
>> stratigraphic diagrams, these are diagrams with a panel for each species
>> showing a time series of abundance, but drawn vertically to represent
>> time passing from bottom of plot towards to top.
>>
>> I am most of the way there with this now, but I want to do away with the
>> strip on each panel and instead draw a custom top axis with a single
>> tick mark (situated at the panel midpoint) with label equal to that
>> which would be used for the strip text. I can do all of this except get
>> the correct label. How do I get access to the factor level being plotted
>> in each panel within my custom axis function?
>>
>> It may be easier to illustrate than explain, so here is a dummy example,
>> including a version of my custom axis function.
>>
>> require(lattice)
>>
>> ## custom axis function
>> axis.VarLabs<- function(side, ...) {
>>     if(isTRUE(all.equal(side, "top"))) {
>>         M<- function(lims) min(lims) + (diff(lims) / 2)
>>         xlim<- current.panel.limits()$xlim
>>         panel.axis(side = side, outside = TRUE, at = M(xlim),
>>                    tck = 1, line.col = "black",
>>                    text.col = "black", rot = 45)
>>     } else {
>>         axis.default(side = side, ...)
>>     }
>> }
>>
>> ## demo data
>> set.seed(123)
>> dat<- data.frame(X = rnorm(1000), Y = rpois(1000, 2),
>>                   fac = sample(gl(4, 500, labels = LETTERS[1:4])))
>> head(dat)
>> str(dat)
>>
>> ## xyplot with custom axis --- note I leave the strip on here to show
>> ## that I want the labels to be A, B, C, D on the top axis ticks...
>> xyplot(Y ~ X | fac, data = dat, axis = axis.VarLabs, layout = c(4,1,1))
>
> # There must a better way, but this works; add
>
>  labels = levels(dat$fac)[panel.number()],

More generally, which.packet() will give you the current indices of
all the conditioning variables. There is no direct access to the
levels, so you need to pass that in separately.

You might also consider this alternative:

set.seed(123)
## longer labels
dat <- data.frame(X = rnorm(1000), Y = rpois(1000, 2),
                  fac = sample(gl(4, 500, labels = month.name[1:4])))

require(grid)

xyplot(Y ~ X | fac, data = dat, strip = FALSE,
       scales = list(x = list(alternating = FALSE, tck = c(1, 0))),
       legend = list(top = list(fun = textGrob(levels(dat$fac),
                                               x = seq(0.125, 0.875,
length = 4),
                                               rot = 45))),
       layout = c(4,1,1))


-Deepayan

>
> # to your panel.axis() call in axis.VarLabs.
>
>> Notice how in this plot, because I have not specified a label the 'at'
>> value for this point is used. Is there a way to get at the factor levels
>> from within an axis function? If so, how?
>>
>> Secondly, how do you ensure there is enough space around the plot to
>> draw the axis labels without truncation - as can be seen on the example
>> xyplot.
>
> # Look at the settings for layout.heights, especially
> # axis.top and top.padding:
>
>  xyplot(....,
>    par.settings = list(layout.heights =
>        list(axis.top = xxx,
>             top.padding = xxx)))
>
> # (Shouldn't need both; I don't know which is more
> # suitable for you.)
>
>  -Peter Ehlers
>
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