[R] drawing a line indicating extent of each factored data series in multipanel lattice xyplot

[Dan Kortschak]

Hi,

Am am plotting aggregated frequency data (extracted from an RDBMS)
relating to DNA sequence features for each of the human chromosomes as
described in the table chromosomes below (the frequency data is in a
table 'hits' that has a value (or not) for each of a set of bins across
each chromosome).

I would like to mark the extent of the chromosome (according to the
length value in chromosome) with a line under the xyplot for each panel
(at the moment - not included in the xyplot statement below - I have
just added the length in bins to the panel strip, but this is not the
best solution for representing the data).

I have tried a couple of approaches to this (example below), but have
not got anything to work (the 100000 value refers to bin size).

Can anyone suggest an approach to accomplish this?

An additional though less significant question is how I can get the
panels to be in the order of the chromosomes as listed in the
chromosomes table rather than alphabetical order of their names.

thanks
Dan

> chromosomes
   chromosome       refSeq                       name    length
1           0  NC_000001.9  Homo sapiens chromosome 1 247249719
2           1 NC_000002.10  Homo sapiens chromosome 2 242951149
3           2 NC_000003.10  Homo sapiens chromosome 3 199501827
4           3 NC_000004.10  Homo sapiens chromosome 4 191273063
5           4  NC_000005.8  Homo sapiens chromosome 5 180857866
6           5 NC_000006.10  Homo sapiens chromosome 6 170899992
7           6 NC_000007.12  Homo sapiens chromosome 7 158821424
8           7  NC_000008.9  Homo sapiens chromosome 8 146274826
9           8 NC_000009.10  Homo sapiens chromosome 9 140273252
10          9  NC_000010.9 Homo sapiens chromosome 10 135374737
11         10  NC_000011.8 Homo sapiens chromosome 11 134452384
12         11 NC_000012.10 Homo sapiens chromosome 12 132349534
13         12  NC_000013.9 Homo sapiens chromosome 13 114142980
14         13  NC_000014.7 Homo sapiens chromosome 14 106368585
15         14  NC_000015.8 Homo sapiens chromosome 15 100338915
16         15  NC_000016.8 Homo sapiens chromosome 16  88827254
17         16  NC_000017.9 Homo sapiens chromosome 17  78774742
18         17  NC_000018.8 Homo sapiens chromosome 18  76117153
19         18  NC_000019.8 Homo sapiens chromosome 19  63811651
20         19  NC_000020.9 Homo sapiens chromosome 20  62435964
21         20  NC_000021.7 Homo sapiens chromosome 21  46944323
22         21  NC_000022.9 Homo sapiens chromosome 22  49691432
23         22  NC_001807.4 Homo sapiens mitochondrion     16571
24         23  NC_000023.9  Homo sapiens chromosome X 154913754
25         24  NC_000024.8  Homo sapiens chromosome Y  57772954


xyplot(hits~bin|chromosomes$name[chromosome+1],
	data=hits,
	horizontal=FALSE,
	origin=0,
	lab=c(3,10),pch=20,cex=0.01,
	layout=c(1,5,5),
	strip=strip.custom(style=3,
		bg="grey90",par.strip.text=list(cex=0.5)),
	as.table=TRUE,
	panel=function(x,y,...,length=chromosomes$length[chromosome+1])
		{panel.xyplot(x,y,...); panel.lines(0,-100,length/100000,-100)}
)