Yes ... that's much better. RTFM, Bert.
-- Bert
On Fri, Jan 18, 2013 at 7:57 AM, Raeanne Miller
<raeanne.mil...@sams.ac.uk> wrote:
> Hi Bert,
>
> Thanks for your answer - I've done a good bit of research in to panel
> functions this afternoon, and they're starting to seem a *little* less
> intimidating. I didn't know there was a panel.lines, so that's very helpful!
>
> Turns out that panel.loess has an argument 'horizontal', which when set to
> 'TRUE' bases the smooth on the y axis, as opposed to the x. So by using a
> panel function:
>
> panel.groups = function(x, y, ..., lty) {
> panel.xyplot(x, y, ...)
> panel.loess(x,y, horizontal=TRUE, lty=lty,...)
> }
>
> in my call to xyplot, it seems I can get the smooth the way I want it, with
> Depth on the y axis and abundance on the x axis.
>
> Hope that is useful for anyone else interested - and Bert, thanks again for
> the swift reply!
>
> Raeanne
>
> -----Original Message-----
> From: Bert Gunter [mailto:gunter.ber...@gene.com]
> Sent: 18 January 2013 15:08
> To: Raeanne Miller
> Cc: r-help@r-project.org
> Subject: Re: [R] lattice: loess smooths based on y-axis values
>
> Reanne:
>
>
> UNTESTED:
>
> I would reverse the xyplot call as xyplot(x~y,...) to get all axes set up
> properly and then just write an explicit panel function using
> loess() and predict.loess the "correct" way, e.g. as loess(y~x) to get the
> (x,y) curve pairs to be plotted via panel.lines(y,x....). You will have to
> make sure the pairs are ordered in decreasing x.
>
> This presumes familiarity with loess() and lattice panel functions, of
> course. Deepayan's book is a comprehensive resource for the latter.
> Murrell's also contains a less comprehensive but probably adequate overview.
> -- If you need anything at all, that is.
>
> -- Bert
>
>
>
> On Fri, Jan 18, 2013 at 3:36 AM, Raeanne Miller <raeanne.mil...@sams.ac.uk>
> wrote:
>> Hi there,
>>
>> I'm using the lattice package to create an xy plot of abundance vs. depth
>> for 5 stages of barnacle larvae from 5 species. Each panel of the plot
>> represents a different stage, while different loess smoothers within each
>> panel should represent different species.
>>
>> However, I would like depth to be on the y-axis and abundance to be on the
>> x-axis, because this is more intuitive as an oceanographer. The smoothing
>> curves would then represent the abundance profiles with depth of the larvae.
>> I have tried just switching depth and abundance in the plot formula/coding,
>> but this means that the loess smoother is based on averaging depth values
>> for each abundance, which means that the curves give multiple possible
>> abundances at each depth level. Rather, I would like the loess smooth to
>> still be based on 'averaging' abundance at each depth.
>>
>> Essentially, I would like a mirror image of the plot from this code:
>>
>> ord<-order(Zoo_nocyp$Depth_m, decreasing=TRUE)
>> xyplot(log10Ab[ord]~factor(-1*Depth_m[ord])|StageF[ord],
>> data=Zoo_nocyp[Zoo_nocyp$log10Ab!="0" ,],
>> type=c("p","smooth"),
>> par.settings=list(strip.background=list(col="white"),
>> fontzize=list(text=16,points=10), lty = 0),
>> space=0, border=NA,
>> col=c("blue","red","green","purple","orange"),
>> stack=TRUE, groups=Zoo_nocyp$SpeciesF,
>> key=
>> list(title="Species",
>> cex.title=1,text=list(c("BB","BC","CH","SB","VS")),space="right",
>> rectangles=list(size=2,
>> border="white",col=c("blue","red","green","purple","orange"))),
>> xlab="depth (m)", ylab="log10 abundance",
>> layout=c(2,3))
>>
>> which is different to what you get when you switch log10Ab and Depth_m.
>>
>> Is there any way to specify the smoothers to be based on sequential y-axis
>> values, rather than x? Or to get the mirror image of a plot?
>>
>> I can provide a dataset offline, for those interested.
>>
>> Thanks very much,
>>
>> Raeanne
>>
>>
>> The Scottish Association for Marine Science (SAMS) is registered in Scotland
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>> (9206). SAMS has an actively trading wholly owned subsidiary company: SAMS
>> Research Services Ltd a Limited Company (SC224404). All Companies in the
>> group are registered in Scotland and share a registered office at Scottish
>> Marine Institute, Oban Argyll PA37 1QA. The content of this message may
>> contain personal views which are not the views of SAMS unless specifically
>> stated. Please note that all email traffic is monitored for purposes of
>> security and spam filtering. As such individual emails may be examined in
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>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
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>> PLEASE do read the posting guide
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>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
> The Scottish Association for Marine Science (SAMS) is registered in Scotland
> as a Company Limited by Guarantee (SC009292) and is a registered charity
> (9206). SAMS has an actively trading wholly owned subsidiary company: SAMS
> Research Services Ltd a Limited Company (SC224404). All Companies in the
> group are registered in Scotland and share a registered office at Scottish
> Marine Institute, Oban Argyll PA37 1QA. The content of this message may
> contain personal views which are not the views of SAMS unless specifically
> stated. Please note that all email traffic is monitored for purposes of
> security and spam filtering. As such individual emails may be examined in
> more detail.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
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