Hi Deepayan, I had a partial victory with xyplot.
Changing chromosome == "chr19" to chromosome == "chr19.fa" indeed fixed the
problem.
I can plot to my screen now doing
xyplot(log(count) ~ nread | sample,
as(gdapply(E1, islandReadSummary), "data.frame"),
subset = (chromosome == "chr19.fa" & nread <= 40),
layout = c(1, 4), pch = 16, type = c("p", "g"))
Its a very nice 4-paneled figure for control 1, control 2, treatment 1 and
treatment 2.
The not so successful story is when I try to plot to an eps file. I do
postscript(file = fileOutputGraph,
horizontal=FALSE,
onefile=FALSE, # needed for EPS output. It is counterintuitive.
paper="letter",
#width=8.5, height=8.5/3,
width=6, height=8.5,
colormodel="rgb")
xyplot(log(count) ~ nread | sample,
as(gdapply(E1, islandReadSummary), "data.frame"),
subset = (chromosome == "chr19.fa" & nread <= 40),
layout = c(1, 4), pch = 16, type = c("p", "g"))
but the eps that is produced has a beheaded top panel and the figure becomes
only black and white.
I can't report any error messages because there are none. I tried to plot to
png or pdf but neither worked, no error messages from R. Only output to eps
worked to some extent.
Can you give some pointer to solve it?
Thank you,
Ivan
----- Original Message ----
From: "[email protected]" <[email protected]>
To: Deepayan Sarkar <[email protected]>
Cc: [email protected]
Sent: Wednesday, 29 April, 2009 0:23:05
Subject: Re: [Bioc-sig-seq] Error while trying to xyplot. Perhaps a lattice
problem.
Hello Deepayan,
Thanks for giving me a hand with xyplot.
The output of str(nread.islands) is
> nread.islands <- as(gdapply(E1, islandReadSummary), "data.frame")
> str(nread.islands)
'data.frame': 4886 obs. of 4 variables:
$ nread : num 1 2 3 4 5 6 7 8 9 10 ...
$ count : num 80871 12722 2548 666 176 ...
$ chromosome: Factor w/ 21 levels "chr1.fa","chr10.fa",..: 1 1 1 1 1 1 1 1 1 1
...
$ sample : Factor w/ 4 levels "C1","C2","T1",..: 1 1 1 1 1 1 1 1 1 1 ...
>
Aha! I see what you mean. Instead of using
chromosome == "chr19"
I should be using
chromosome == "chr19.fa"
Now I am logged in remotely to my work computer. Bad connection. I'll try it
tomorrow and let you know if it works.
Thank you.
Ivan
----- Original Message ----
From: Deepayan Sarkar <[email protected]>
To: [email protected]
Cc: [email protected]
Sent: Tuesday, 28 April, 2009 19:01:16
Subject: Re: [Bioc-sig-seq] Error while trying to xyplot. Perhaps a lattice
problem.
On Tue, Apr 28, 2009 at 9:58 AM, <[email protected]> wrote:
>
> Hello everybody,
>
> I am working with the yet unreleased package chipseq.
>
> There is a very nice xyplot that I am trying to reproduce from the
>
> http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/ChipSeqWorkflow.pdf
>
> However, R complains saying
>
> "Error in limits..and.aspect(prepanel.default.xyplot, prepanel = prepanel, :
> need at least one panel"
>
> What am I doing? This
>
>> class(E1)
> [1] "GenomeDataList"
> attr(,"package")
> [1] "BSgenome"
>> names(E1)
> [1] "C1" "C2" "T1" "T2"
>> islandReadSummary <- function(x)
> + {
> + g <- extendReads(x, seqLen = 200)
> + s <- slice(coverage(g, 1, max(end(g))), lower = 1)
> + tab <- table(viewSums(s) / 200)
> + ans <- data.frame(nread = as.numeric(names(tab)), count = as.numeric(tab))
> + ans
> + }
>> nread.islands <- as(gdApply(E1, islandReadSummary), "data.frame")
> There were 50 or more warnings (use warnings() to see the first 50)
Could you share the output of
str(nread.islands)
?
>> xyplot(log(count) ~ nread | sample,
> + nread.islands,
> + subset = (chromosome == "chr19" & nread <= 40),
> + layout = c(1, 4), pch = 16, type = c("p", "g"))
> Error in limits..and.aspect(prepanel.default.xyplot, prepanel = prepanel, :
> need at least one panel
>>
>
> Can anybody shed some light?
>
> Clarification: the warning "There were 50 or more warnings (use warnings() to
> see the first 50)" comes from IRanges. chipseq is using the slightly older
> start/end convention rather than the newer shift/step convention.
>
Actually, that's happening inside your 'islandReadSummary' function, where
s <- slice(coverage(g, 1, max(end(g))), lower = 1)
should now be
s <- slice(coverage(g), lower = 1)
-Deepayan
> Thank you,
>
> Ivan
>
>
>
>
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>
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