On Oct 13, 2010, at 10:05 AM, Christophe Bouffioux wrote:
Dear R-community,
Using bwplot, how can I put the whiskers at percentile 5 and
percentile 95,
in place of the default position coef=1.5??
Using panel=panel.bwstrip, whiskerpos=0.05, from the package
agsemisc gives
satisfaction, but changes the appearance of my boxplot and works
with an old
version of R, what I dont want, and I didnt find the option in
box.umbrella parameters
Nope, you won't find it even if you search harder, but you do have a
lattice path forward. Just as base function boxplot() does the
calculations and then plots with bxp(), by default panel.bwplot sends
the data to boxplot.stats, but panel.bwplot also allows you to specify
an alternate function that returns plotting parameters differently as
long as those conforms to the requirements for structure. You can look
at boxplot.stats (it's not that big) and then construct an
alternative. The line you would need to alter would be the one
starting with: stats<-stats::fivenum(...), since you are changing the
values returned by fivenum(). You might get away with just changing
stats[1] and stats[5] to your revised specifications, although it has
occurred to me that you might get some of those "out" dots inside your
whiskers. (Fixing that would not be too hard once you are inside
boxplot.stats().
Seemed to work for me with your data (at least the extent of plotting
a nice 3 x 2 panel display. All I did was redefine an nboxplot.stats
by inserting this line after the line cited above:
stats[c(1,5)]<- quantile(x, probs=c(0.05, 0.95))
and then added an argument ..., stats=nboxplot.stats) inside your
panel.bwplot.
--
David.
Many thanks
Christophe
Here is the code:
library(lattice)
ex <- data.frame(v1 = log(abs(rt(180, 3)) + 1),
v2 = rep(c("2007", "2006", "2005"), 60),
z = rep(c("a", "b", "c", "d", "e", "f"), e = 30))
ex2 <- data.frame(v1b = log(abs(rt(18, 3)) + 1),
v2 = rep(c("2007", "2006", "2005"), 6),
z = rep(c("a", "b", "c", "d", "e", "f"), e = 3))
ex3 <- merge(ex, ex2, by=c("v2","z"))
D2007 <- ex3[ex3$z=="d" & ex3$v2==2007, ]
D2006 <- ex3[ex3$z=="d" & ex3$v2==2006, ]
C2007 <- ex3[ex3$z=="c" & ex3$v2==2007, ]
quantile(D2007$v1, probs = c(0.05, 0.95))
quantile(D2006$v1, probs = c(0.05, 0.95))
quantile(C2007$v1, probs = c(0.05, 0.95))
bwplot(v2 ~ v1 | z, data = ex3, layout=c(3,2), X = ex3$v1b,
pch = "|",
par.settings = list(
plot.symbol = list(alpha = 1, col = "transparent",cex = 1,pch = 20)),
panel = function(x, y, ..., X, subscripts){
panel.grid(v = -1, h = 0)
panel.bwplot(x, y, ..., subscripts = subscripts)
X <- X[subscripts]
xmax =max(x)
X <- tapply(X, y, unique)
Y <- tapply(y, y, unique)
tg <- table(y)
panel.points(X, Y, cex=3, pch ="|" , col = "red")
#vcount <- tapply(v1, v2, length)
panel.text((xmax-0.2), (Y-0.15), labels = paste("N=", tg))
})
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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
