[BioC] chromosome ordering in cPlot()/cColor()
Martin Morgan
mtmorgan at fhcrc.org
Wed Aug 26 19:18:45 CEST 2009
Hi Axel --
Axel.Klenk at Actelion.Com wrote:
> Hi Martin,
>
> thanks a lot for your help. I have tested your workaround on my data set
> and it produces the desired result -- thanks for pointing me to
> initialize()...
initialize() is a low-level function, so think of this as a 'hack'.
> I have not (yet :-)) observed any unwanted consequences of this change
> but unfortunately have stumbled over two more issues for which I have to
> ask for your assistance:
>
>> library("geneplotter")
>> example(cPlot)
>
> cPlot> ## A bit of a hack to not have a package dependency on hgu95av2
> cPlot> ## but need to fiddle w/ the warn level to not fail the example
> anyways.
> cPlot>
> cPlot> curWarn <- options(warn=0)
>
> cPlot> on.exit(options(warn=curWarn), add=TRUE)
> Error in options(warn = curWarn) : invalid value for 'warn'
>
> Clearly, the example code should read
> on.exit(options(curWarn), add=TRUE)
> or am I mistaken? I admit I am two minor R releases behind (see
> sessionInfo()
> below) but for me example(cPlot) does work neither on WinXP nor on RHEL4
> 64bit.
> But to get object 'z' I can run:
yes I came across that yesterday and fixed it in the 'devel' version of
this package; should have warned you, sorry.
>
>> example(cColor)
> [...]
>
>> objects()
> [1] "curWarn" "probes" "probes2" "z"
>
>> p <- probes2[2:4]
>
>> mget(p, probesToChrom(z))
> $`41807_at`
> [1] "9"
>
> $`931_at`
> [1] "13"
>
> $`39032_at`
> [1] "13"
>
>> cPlot(z, glen = 0.3)
>> cColor(p, c("red", "black", "black"), z, glen = 0.6)
>>
>
> Given that p contains probe names that are mapped to chr 9, 13, and 13 I
> had
> expected a red bar on chr 9 and two black bars on chr 13 -- however, I see
> a
> red bar on chr 9 and a black and a red bar on chr 13... maybe my
> expectation
> is just wrong?
I think plotting in multiple colors is meant to be supported by multiple
calls to cColor, first with probes to be colored "red", then with probes
to be collored "black". The development version has been updated to
support multiple color specifications.
Martin
> (This is of course a hopefully reproducible toy example -- I first observed
> this
> behaviour when mapping fold changes to chromosomes and a region known
> to be all down came out pretty multicoloured.)
>
> This is obviously without applying any workaround on chromosome order etc.
> and the results is the same when chromosomes are reordered.
>
> Can you reproduce/confirm this?
>
> library("geneplotter")
> example(cPlot)
> example(cColor)
> objects()
> p <- probes2[2:4]
> mget(p, probesToChrom(z))
> cPlot(z, glen = 0.3)
> cColor(p, c("red", "black", "black"), z, glen = 0.6)
>
> Could you please let me know if this is the expected result or not ?
>
> Thanks in advance,
>
> - axel
>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC_MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerland.1252
>
> attached base packages:
> [1] datasets stats graphics grDevices utils methods base
>
> other attached packages:
> [1] hgu95av2.db_2.2.12 RSQLite_0.7-1 DBI_0.2-4
> fortunes_1.3-6
> [5] limma_2.18.0 sfsmisc_1.0-7 geneplotter_1.22.0
> lattice_0.17-25
> [9] annotate_1.22.0 AnnotationDbi_1.6.0 Biobase_2.4.1
> MASS_7.2-47
> [13] RODBC_1.2-5 gmodels_2.15.0
>
> loaded via a namespace (and not attached):
> [1] gdata_2.4.2 grid_2.9.0 gtools_2.6.1
> RColorBrewer_1.0-2
> [5] xtable_1.5-5
>
>
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
> Switzerland
>
>
>
>
> Martin Morgan
> <mtmorgan at fhcrc.o
> rg> To
> Sent by: Axel.Klenk at actelion.com
> bioconductor-boun cc
> ces at stat.math.eth bioconductor at stat.math.ethz.ch
> z.ch Subject
> Re: [BioC] chromosome ordering in
> cPlot()/cColor()
> 25.08.2009 18:44
>
>
>
>
>
>
>
>
>
> Martin Morgan <mtmorgan at fhcrc.org> writes:
>
>> Hi Axel --
>>
>> Axel.Klenk at Actelion.Com writes:
>>
>>> Dear Biocore Team,
>>>
>>> I'm using cPlot()/cColor() from package annotate to produce chromosome
>>> plots and
>>> am very impressed how easily this can be achieved. However,
> unfortunately,
>>> the
>>> chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11,
> etc.
>>> from bottom
>>> to top and I would like to reorder them to 1, 2, 3, ... from top to
> bottom
>>> but cannot find an
>>> easy way to do so... am I missing something here?
>>>
>>> I managed to get what I want by hacking buildChromLocation() but that's
>>> ugly and I don't
>>> want to maintain a modified function if not necessary.
>>>
>>> Would it be possible to add a replace method for the chromInfo slot to
>>> allow e.g.
>>>
>>> z <- buildChromLocation("hgug41112a")
>>> library("gtools") # for mixedsort()
>>> info <- chromInfo(z)
>>> chromInfo(z) <- info[rev(mixedsort(names(info)))]
>>>
>>> or maybe you can think of a better solution?
>> As a work-around, you might try
>>
>> example(cPlot) # get object z
>> idx <- c("1", "5", "10", "X")
>> zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx])
>
> oops, that should be
>
> zz <- initialize(z, chromLocs=chromLocs(z)[idx],
> chromInfo=chromInfo(z)[idx])
>
>> cPlot(zz)
>>
>> I'm not sure whether there are other consequences of this sort of
>> change, and if there are it would be good if you would let me know
>> before a more permanent solution is implemented.
>>
>> Martin
>>
>>> Thanks in advance,
>>>
>>> - axel
>>>
>>>
>>> Axel Klenk
>>> Research Informatician
>>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
>>> Switzerland
>>>
>>>
>>>
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> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
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