thank you all for your helpful replies

to bert
the problem with relation ="same" is the plotting along y axis of all 
categories ("samp.time") for all groups ("sites"); instead, I need to 
plot along y axis just the categories for each group effectively having 
a corresponding observation

to danny
your solution with ggplot works like a charm; I will keep an eye to 
ggplot2 for other new charts but for some reasons now I must stick on 
lattice (which is also my favourite by the way)

to richard
result3 is close to what I need but still not exactly what I’m aiming to;
I need y axis to be plotted as categories not as a continuous scale…
I need the result proposed by danny to be translated into lattice…

to deepayan
thank you so much, I’ll carefully consider your hint and I’ll try to 
make it works (but still I’m not sure I fully understand how to do it);
as long as I can get to a viable solution I’ll post it back


Just for your information my effort up to now (NOT WORKING!) was 
pointing toward this direction:
1- new character variable from samp.time to be used later as label for 
the plot:
test$samp.lab<-as.character(test$samp.time)

2- new factor variable with as many levels as the observations:
test$samp.id <- gl(length(test$samp.time), 1)

3- new factor variable based on “samp.time” but with the order of levels 
based on “site”, something like this (I think this is the crucial point 
where I'm likely to fail):
test$samp.time.site <- with(test, reorder(samp.time, as.numeric(site)))

4- new numeric level:
nl <- as.numeric(levels(test$samp.time.site))

5- plotting (wrong):
dotplot(samp.time~conc|site, data=test,
ylim=test$samp.lab[nl],
scales=list(x=list(log=10), y = list(relation = "free")),
layout=c(1,5), strip=FALSE, strip.left=TRUE
)

Il 21/09/2012 08:55, Deepayan Sarkar ha scritto:
> On Thu, Sep 20, 2012 at 7:48 PM, maxbre<mbressan@arpa.veneto.it>  wrote:
>> my reproducible example
>>
>> test<-structure(list(site = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 2L,
>> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L,
>> 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
>> 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L), .Label = c("A",
>> "B", "C", "D", "E"), class = "factor"), conc = c(2.32, 0.902,
>> 0.468, 5.51, 1.49, 0.532, 0.72, 0.956, 0.887, 20, 30, 2.12, 0.442,
>> 10, 50, 110, 3.36, 2.41, 20, 70, 3610, 100, 4.79, 20, 0.0315,
>> 30, 60, 1, 3.37, 80, 1.21, 0.302, 0.728, 1.29, 30, 40, 90, 30,
>> 0.697, 6.25, 0.576, 0.335, 20, 10, 620, 40, 9.98, 4.76, 2.61,
>> 3.39, 20, 4.59), samp.time = structure(c(2L, 4L, 4L, 4L, 4L,
>> 4L, 5L, 4L, 8L, 8L, 8L, 8L, 8L, 9L, 8L, 7L, 8L, 8L, 8L, 8L, 3L,
>> 3L, 2L, 4L, 4L, 4L, 4L, 4L, 1L, 4L, 6L, 4L, 8L, 4L, 8L, 4L, 3L,
>> 8L, 4L, 8L, 4L, 8L, 4L, 9L, 3L, 8L, 8L, 8L, 8L, 8L, 8L, 1L), .Label = c("2",
>> "4", "12", "24", "96", "135", "167", "168", "169"), class = "factor")),
>> .Names = c("site",
>> "conc", "samp.time"), row.names = c(NA, 52L), class = "data.frame")
>>
>>
>>
>> dotplot(samp.time~conc|site, data=test,
>>          scales=list(x=list(log=10), y = list(relation = "free")),
>>          layout=c(1,5), strip=FALSE, strip.left=TRUE
>>          )
>>
>>
>> my objective is to use “site” as conditioning variable but with “samp.time”
>> correctly grouped by “site”; the problem here is to ensure that levels of
>> “samp.time” within each “site” are contiguous as otherwise they would be not
>> contiguous in the dot plot itself (i.e, avoid that sort of holes in between
>> y axis categories -see dotplot -)
>>
>>
>> I’ve been trying with this but without much success
>>
>> test$samp.time.new<-
>>    with(test,reorder(samp.time,as.numeric(site)))
>>
>>
>> dotplot(samp.time.new~conc|site, data=test,
>>          scales=list(x=list(log=10), y = list(relation = "free")),
>>          layout=c(1,5), strip=FALSE, strip.left=TRUE
>>          )
>>
>> I think (I hope) a possible different solution is to create for "ylim" a
>> proper character vector of different length to pass to each panel of the
>> dotplot (I’m not posting this attempt because too much confused up to now)
>>
>> can anyone point me in the right direction?
> The problem here is that there is crossing between sites and
> samp.time. You can try some imaginative permutations of site, such as
>
> test$samp.time.new <- with(test, reorder(samp.time,
> as.numeric(factor(site, levels = c("A", "C", "D", "B", "E")))))
>
> which gets all but site B right. There may be another permutation that
> works for everything, but it would be much easier to make a nested
> factor, i.e.,
>
> test$samp.time.new <- with(test, reorder(samp.time:site, as.numeric(site)))
>
> That just leaves getting the y-labels right, which I will leave for
> you to figure out.
>
> (Hint: ylim = some_function_of(levels(test$samp.time.new)))
>
> -Deepayan
>



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