[BioC] lattice and base-graphics using gridBase

[Maarten van Iterson]

Hi Paul Murrell, 

Thanks for your reply this is exactly what I was looking for. 
To answer your question: I prefer the default graphical parameters of
the boxplot-function and tried to reproduce these using the bwplot (and
trellis.par.set) but didn't succeed and thought that combining both was
maybe easier?

In the future I will post questions like these on the R-help listserv.

Cheers, 

Maarten
 
On Wed, 2010-05-12 at 16:42 +1200, Paul Murrell wrote:
> Hi
> 
> On 5/12/2010 12:54 AM, James W. MacDonald wrote:
> > Hi Maarten,
> >
> > Maarten van Iterson wrote:
> >> Dear list,
> >>
> >> I'm trying to combine lattice and base-graphics following the example
> >> from Paul Murrell's R Graphics (B.1.2).
> >>
> >> The question I have is how to add the y-axis from the base-graphics to
> >> the lattice plot below?
> >
> > Neither of these packages are part of Bioconductor, so I think you would
> > be better served asking this question on the R-help listserv.
> 
> Agreed, but since we're here already ...
> 
> This code should work:
> 
> boxplot.panel <- function(x, y, subscripts, ...){	
>        par(plt=gridPLT(), new=TRUE, ps=8)
>        boxplot(data[[subscripts]], col=rep(2:7, each=2),
>                ylab="", axes=FALSE,
>                names=NULL, outline=FALSE)
>        axis(2)
> }
> 
> df <- data.frame(y=1:3, x=1:3, Method=LETTERS[1:3])
> 
> plot.new()
> xyplot(y ~ x | Method, data=df, subscripts=TRUE, xlab="", ylab="",
>         scales=list(draw=FALSE),
>         panel=boxplot.panel, layout=c(1,3))
> 
> Note that I have taken out the pushing and popping of viewports (so that 
> when the boxplot axis is drawn it lines up with the panel border) and 
> added axis(2) to draw the axis (and specified 'scales' in xyplot() to 
> suppress the lattice axes).  I have also added plot.new() just before 
> the call to xyplot(), which makes sure that the base graphics system is 
> set up (so you don't get the warning).
> 
> But one question for you:  why do you want to use boxplot() instead of 
> bwplot() ?
> 
> Paul
> 
> > Best,
> >
> > Jim
> >
> >
> >>
> >> library(gridBase)
> >> library(lattice)
> >>
> >> data<- list(A=matrix(rnorm(8*100, 1, 1), ncol=8), B=matrix(rnorm(8*100,
> >> 0, 1), ncol=8), C=matrix(rnorm(8*100, -1, 1), ncol=8))
> >>
> >> boxplot.panel<- function(x, y, subscripts, ...){	
> >> 	pushViewport(viewport(gp=gpar(fontsize=8)),
> >>                 viewport(y=unit(0.95, "npc"), width=0.9,
> >> height=unit(0.95, "npc"), just="top"))
> >>    par(plt=gridPLT(), new=TRUE, ps=8)
> >> 	boxplot(data[[subscripts]], col=rep(2:7, each=2), ylab="", axes=FALSE,
> >> names=NULL, outline=FALSE)
> >>    popViewport(2)
> >> }
> >>
> >> df<- data.frame(y=1:3, x=1:3, Method=LETTERS[1:3])
> >>
> >> xyplot(y ~ x | Method, data=df, subscripts=TRUE, xlab="", ylab="",
> >> panel=boxplot.panel, layout=c(1,3))
> >>
> >> sessionInfo()
> >> R version 2.10.0 (2009-10-26)
> >> x86_64-unknown-linux-gnu
> >>
> >> locale:
> >>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> >>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] grid      stats     graphics  grDevices utils     datasets
> >> methods
> >> [8] base
> >>
> >> other attached packages:
> >> [1] lattice_0.17-26 gridBase_0.4-3
> >>
> >> Thanks in advance,
> >>
> >> Maarten
> >>
> >>
> >
> 


-- 
Maarten van Iterson
Center for Human and Clinical Genetics
Leiden University Medical Center (LUMC)
Research Building, Einthovenweg 20 
Room S-04-038
Phone: 071-526 9439
E-mail: M.van_iterson.HG at lumc.nl
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