Sweave: infelicities with lattice graphics

Just a follow-up on this thread, now with R 2.11.1.  I was happy back 
then to use Deepayan's solution for this, under earlier R versions; but 
it now gives an error and the Sweave-generated .tex file no longer compiles.

<<ortho-xyplot1-code, keep.source=TRUE, eval=FALSE>>=
library(nlme)
library(lattice)
xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, 
pch=15:25,
     col=palette(), cex=1.3, main="Orthodont data")
@
<<ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6>>=
plot(trellis.last.object())
@

Now, I get the following from Sweave:

Error:  chunk 46 (label=ortho-xyplot1)
Error in !lattice.getStatus("current.plot.saved", prefix = prefix) :
   invalid argument type

Did something in lattice change so that plot(trellis.last.object()) no 
longer works or needs to be specified differently?

-Michael



On 7/16/2010 1:14 AM, Deepayan Sarkar wrote:

On Thu, Jul 15, 2010 at 1:51 PM, Michael Friendly<friendly at yorku.ca>  wrote:

In a paper I'm writing using Sweave, I make use of lattice graphics, but
don't want to explicitly show (or explain)
in the article text the print() wrapper I need in code chunks for the graphs
to appear. I can solve this by including each chunk twice, with different
options, as in

<<ortho-xyplot1-code, keep.source=TRUE, eval=FALSE>>=
library(nlme)
library(lattice)
xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject,
pch=15:25,
   col=palette(), cex=1.3, main="Orthodont data")
@
<<ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6>>=
library(nlme)
library(lattice)
print(xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject,
pch=15:25,
   col=palette(), cex=1.3, main="Orthodont data"))
@

but then, if I decide to change the plotting code, I have to make changes in
two places.  Is there some
feature of Sweave or lattice I've missed that would simplify this? Re-use of
code chunks doesn't seem
to apply here.

I usually use this variant of Duncan's suggestion:

<<ortho-xyplot1-code, keep.source=TRUE, eval=FALSE>>=
library(nlme)
library(lattice)
xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25,
   col=palette(), cex=1.3, main="Orthodont data")
@

<<ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6>>=
plot(trellis.last.object())
@

-Deepayan

On 12/09/2010 11:41 AM, Michael Friendly wrote:

Just a follow-up on this thread, now with R 2.11.1.  I was happy back then
to use Deepayan's solution for this, under earlier R versions; but it now
gives an error and the Sweave-generated .tex file no longer compiles.

<<ortho-xyplot1-code, keep.source=TRUE, eval=FALSE>>=
library(nlme)
library(lattice)
xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject,
pch=15:25,
    col=palette(), cex=1.3, main="Orthodont data")
@
<<ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6>>=
plot(trellis.last.object())
@

Now, I get the following from Sweave:

Error:  chunk 46 (label=ortho-xyplot1)
Error in !lattice.getStatus("current.plot.saved", prefix = prefix) :
  invalid argument type

Did something in lattice change so that plot(trellis.last.object()) no
longer works or needs to be specified differently?

I don't know if something in lattice has changed, but that doesn't look as
though it should work:  the code to do the plot was never evaluated.  I
think you would need eval=TRUE in the first chunk, or
<<ortho-xyplot1-code>>
ahead of the plot command in the second.

On Sun, Sep 12, 2010 at 8:47 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
  

On 12/09/2010 11:41 AM, Michael Friendly wrote:
    

Just a follow-up on this thread, now with R 2.11.1.  I was happy back then
to use Deepayan's solution for this, under earlier R versions; but it now
gives an error and the Sweave-generated .tex file no longer compiles.

<<ortho-xyplot1-code, keep.source=TRUE, eval=FALSE>>=
library(nlme)
library(lattice)
xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject,
pch=15:25,
    col=palette(), cex=1.3, main="Orthodont data")
@
<<ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6>>=
plot(trellis.last.object())
@

Now, I get the following from Sweave:

Error:  chunk 46 (label=ortho-xyplot1)
Error in !lattice.getStatus("current.plot.saved", prefix = prefix) :
  invalid argument type

Did something in lattice change so that plot(trellis.last.object()) no
longer works or needs to be specified differently?
      

I don't know if something in lattice has changed, but that doesn't look as
though it should work:  the code to do the plot was never evaluated.  I
think you would need eval=TRUE in the first chunk, or
<<ortho-xyplot1-code>>
ahead of the plot command in the second.
    

Yes. I notice that it was me who introduced the eval=FALSE (I'm not
sure why). Hopefully that should fix it.

However, there _has_ been a recent lattice update, where the internals
have undergone some change, so there is a chance that is to blame. I
won't be able to take a look before day after tomorrow.

-Deepayan