Palette color order in bwplot (lattice violin plot) vs. boxplot

Hello,

I am trying to give different colors to boxes in a violin plot obtained via
bwplot from lattice package using a color palette from RColorBrewer:

require(RColorBrewer)
MyPalette <- brewer.pal(6, "Set3")

A call to:

boxplot(count ~ spray, data = InsectSprays, col = MyPalette)

yields the example boxplot with each box colored according to the different
colors from MyPalette. In addition, boxes are colored with the same color
order of MyPalette. See

display.brewer.pal(6, "Set3")

However, when I do the same thing with a violin plot from the lattice
package

require(lattice)
bwplot(count ~ spray, data = InsectSprays,

+ ? ? ? ?panel = function(..., box.ratio) {
+ ? ? ? ? ? ?panel.violin(..., col = "transparent",
+ ? ? ? ? ? ? ? ? ? ? ? ? varwidth = FALSE, box.ratio = box.ratio)
+ ? ? ? ? ? ?panel.bwplot(..., fill = MyPalette, box.ratio = .1)
+ ? ? ? ?} )

boxplots are colored with the right colors (each box has a different color)
but with a different color order -- too bad because I would like to color
code the plot according to certain pre-defined colors. Same thing (wrong
color order) with a simple bwplot:

bwplot(count ~ spray, data = InsectSprays, fill = MyPalette)

Is there a way to get the right color (i.e. same order as in MyPalette) in
bwplot/panel.violin?

On 04/04/2010 06:21, Deepayan Sarkar wrote:

On Thu, Apr 1, 2010 at 4:10 AM, Luigi Ponti <lponti at inbox.com> wrote:

Hello,

I am trying to give different colors to boxes in a violin plot obtained via
bwplot from lattice package using a color palette from RColorBrewer:
[...]
However, when I do the same thing with a violin plot from the lattice
package

require(lattice)
bwplot(count ~ spray, data = InsectSprays,

+ ? ? ? ?panel = function(..., box.ratio) {
+ ? ? ? ? ? ?panel.violin(..., col = "transparent",
+ ? ? ? ? ? ? ? ? ? ? ? ? varwidth = FALSE, box.ratio = box.ratio)
+ ? ? ? ? ? ?panel.bwplot(..., fill = MyPalette, box.ratio = .1)
+ ? ? ? ?} )

boxplots are colored with the right colors (each box has a different color)
but with a different color order -- too bad because I would like to color
code the plot according to certain pre-defined colors. Same thing (wrong
color order) with a simple bwplot:

bwplot(count ~ spray, data = InsectSprays, fill = MyPalette)

Is there a way to get the right color (i.e. same order as in MyPalette) in
bwplot/panel.violin?

The correct approach would be along the lines of

bwplot(count ~ spray, data = InsectSprays,
? ? ? ?groups = spray,
? ? ? ?panel = panel.superpose,
? ? ? ?panel.groups = panel.violin,
? ? ? ?col = MyPalette)

(unlike panel.xyplot etc., panel.bwplot does not explicitly handle grouping).

Thanks! This way I get violin plots colored in the correct order.
However, I lose control on panel.violin -- not sure if/how I can regain
that (i.e., the stuff the was done by the panel = function(){} above).

Also, I have noticed that violin plots extend beyond the data range: is
this the default behavior? In ?panel.violin and ?density, I read that
default parameters should allow "the estimated density to drop to
approximately zero at the extremes". For example, the minimum value of
the "count" variable (data = InsectSprays) is zero, but the violin plots
do extend below zero. Am I missing something?

Thanks for the hint, Felix: the following code makes it but (don't know why)
the median dots disappear.

bwplot(count ~ spray, data = InsectSprays,
?????? groups = spray,
?????? panel = panel.superpose,
?????? panel.groups =? function(..., box.ratio) {
??????????? panel.violin(...,
???????????????????????? varwidth = FALSE, box.ratio = box.ratio, cut = 0)
??????????? panel.bwplot(..., box.ratio = .1)
??????? },
??????? fill = MyPalette
)

I tried to change box.dot parameter to no avail. Not sure what is going on
here. It would appear that the panel.groups = function(){} is not sure where
to read graphical parameters from (just guessing). It would be interesting
to know your opinion.