[R] superpose.polygon, panel.polygon and their colors

ottorino ottorino-luca.pantani at unifi.it
Tue Oct 19 18:29:02 CEST 2010

```Dear R-helpers,
the problem I'm facing today is to convince lattice to paint some areas
in gray.
The areas I would like to have in gray, are confidence bands

I've googled around in the mailing list archives and eventually find
some clues.

This link is my starting point
http://tolstoy.newcastle.edu.au/R/e2/help/07/04/15595.html

I'm reproducing here the code for your convenience

est <- c(1:4, 3:6, 7, 9, 11, 13, 12, 15, 18, 21)
cond <- rep(c('a','b'), each = 8)
grp <- rep(c('I', 'II'), each = 4, 2)
x <- rep(c(.5, .7, .9, 1.1), 4)
upper <- est + 1
lower <- est - 1
data <- data.frame(est = est, x = x, cond = cond, grp = grp, upper =
upper, lower = lower)
rm(est, cond, grp, x, upper,lower)

panel.bands <-

function(x, y, upper, lower,

subscripts, col, ..., font, fontface) {

upper <- upper[subscripts]
lower <- lower[subscripts]
panel.polygon(c(x, rev(x)), c(upper, rev(lower)),...) }

xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'panel.bands',...)
panel.xyplot(x, y, ...)
})

The result is a lattice object with the confidence bands painted in cyan
and pink. These are the areas I would like to have in gray.

I think that the cyan and pink colors come from

trellis.par.get("superpose.polygon")[[2]][1:2]

To change the colors I tried, unsuccessfully, the following 4 ways:

1)
trellis.par.set("superpose.polygon", list(col="gray"))
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'panel.bands',...)
panel.xyplot(x, y, ...)
})

2)
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'panel.bands',
col="gray", ...)
panel.xyplot(x, y, ...)
})

3)
ltheme <- canonical.theme(color = FALSE)
ltheme\$superpose.polygon\$col="gray"
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
theme=ltheme,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'panel.bands',...)
panel.xyplot(x, y, ...)
})

4)
panel.bands.1 <-

function(x, y, upper, lower,

subscripts, col, ..., font, fontface) {

upper <- upper[subscripts]
lower <- lower[subscripts]
panel.polygon(c(x, rev(x)), c(upper, rev(lower)),
col="gray", ...) }

xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
panel = function(x, y, ...){
panel.superpose(x, y,
panel.groups = 'panel.bands.1',...)
panel.xyplot(x, y, ...)
})

I suspect that superpose polygon is not involved at all in the process,
and in

test.gray <-
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'panel.bands',...)
panel.xyplot(x, y, ...)
})
str(test.gray)

I cannot find any indication on the colors.

Strangely enough, the following code seems to modify something,
the border of the colored areas.

panel.bands.2 <-

function(x, y, upper, lower,

subscripts, col, ..., font, fontface) {

upper <- upper[subscripts]
lower <- lower[subscripts]
panel.polygon(c(x, rev(x)), c(upper, rev(lower)),
border= 2, ...) }

xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data\$upper,
lower = data\$lower,
panel = function(x, y, ...){
panel.superpose(x, y,
panel.groups = 'panel.bands.2',...)
panel.xyplot(x, y, ...)
})

In other words I can modify the borders, but not the shaded areas.
This sounds strange to me.
Where am I wrong ?

--
Ottorino-Luca Pantani, Università di Firenze
Dip.to di Scienze delle Produzioni Vegetali,
del Suolo e dell'Ambiente Forestale (DiPSA)
P.zle Cascine 28 50144 Firenze Italia
Ubuntu 10.04 -- GNU Emacs 23.1.50.1 (x86_64-pc-linux-gnu, GTK+ Version
2.18.0)
ESS version 5.8 -- R 2.10.1

```