[R] how to specify the order of panels with xyplot

Dan Kortschak dan.kortschak at adelaide.edu.au
Fri Nov 20 08:23:54 CET 2009


I have sorted out how to do this - by much trial an error (a comment
from Deepayan in a post some years ago pointed which way to go, though
it took a lot of searching to find even where to start with it:

I've bound the two sets of data together, making the relevant part an
ordered factor. It's probably not the nicest way to do it, but it works.

hits<-cbind(hits,chromosomes$name[hits$Chromosome])
names(hits)[5]<-'name'
hits$name<-factor(hits$name,ordered(chromosomes$name[1:dim(chromosomes)[1]]))
xyplot(weighted~bin|name,data=hits)


On Fri, 2009-11-20 at 12:16 +1030, Dan Kortschak wrote:
> > chromosomes
>    id       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$name[Chromosome+1],data=hits,horizontal=FALSE,origin=0,lab=c(3,10),pch=20,cex=0.01,layout=c(1,5,5),strip=strip.custom(style=3,bg="grey90",par.strip.text=list(cex=0.5)),as.table=TRUE)
> 
> 
> I am wondering how to reorder the panels such that they are plotted in
> the order of chromosomes$id rather than chromosomes$name. I am sure that
> this has been answered in the past, but I am finding it difficult to
> understand (I have looked at factor and reorder.factor).
> 
> (I've had a look at strip.custom to see if I can get what I want with
> that, and it looks like I should be able to, but I can't figure out
> how).
> 
> thanks
> Dan



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