R help - Sep 2007 - plotting predicted curves with log scale in lattice

Excuse me for forgetting sessionInfo (below)
Ken Knoblauch <knoblauch <at> lyon.inserm.fr>
writes:
> I was taken off guard by the following behavior in a lattice plot.
> I frequently want to add a predicted curve defined at more
> points than in the formula expression of xyplot.  There have
> been numerous examples of how to do this on r-help, but I
> still often struggle to make this work.  I just realized that
> specifying one of the axes on a log scale does not guarantee
> that the added data for a curve will automatically take that
> into account.  I don't know if this should be called a bug,
> I haven't picked up an indication that would lead me to
> expect this in the documentation.  I admit that if I had a
> deeper understanding of lattice and/or grid, it might be
> clearer why...  Here is a toy example illustrating the behavior
> (there may be a more efficient way to do this),
> 
> ds1 <- data.frame( RR = rep(seq(0, 1, len = 5)^2, 2) +
> 						rnorm(10, sd = 0.1),
> 				   LL = rep(10^seq(1, 5), 2),
> 				   FF = factor(rep(letters[1:2], each = 5))
> 				   )
> ds2 <- data.frame(RR = rep(seq(0, 1, len = 20)^2, 2),
> 				  LL = rep(10^seq(1, 5, len = 20), 2),
> 				   FF = factor(rep(letters[1:2], each = 20))
> 				   )
> library(lattice)
> xyplot(RR ~ LL | FF, ds1,
> 		scales = list(x = list(log = TRUE)),
> 		aspect = "xy",
> 		subscripts = TRUE,
> 		ID = ds2$FF,
> 		panel = function(x, y, subscripts, ID, ...) {
> 			w <- unique(ds1$FF[subscripts])
> 			llines(log10(ds2$LL[ID == w]), ds2$RR[ID == w], ...)
> 			panel.xyplot(x, y, ...)
> 			}
> 		)
> 
> Note that the x-variable of llines must be logged to plot the correct
values
> and so the scales argument seems to apply only to the x, y arguments
> passed to the panel function.
R version 2.5.1 Patched (2007-08-26 r42657) 
i386-apple-darwin8.10.1 

locale:
C

attached base packages:
[1] "stats"     "graphics"  "grDevices"
"utils"     "datasets"  "methods"
[7] "base"     

other attached packages:
 lattice 
"0.16-3" 

but this also occurs for
R version 2.6.0 Under development (unstable) (2007-08-26 r42657) 
i386-apple-darwin8.10.1 

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lattice_0.16-3

loaded via a namespace (and not attached):
[1] grid_2.6.0

Hi,

I was taken off guard by the following behavior in a lattice plot.
I frequently want to add a predicted curve defined at more
points than in the formula expression of xyplot.  There have
been numerous examples of how to do this on r-help, but I
still often struggle to make this work.  I just realized that
specifying one of the axes on a log scale does not guarantee
that the added data for a curve will automatically take that
into account.  I don't know if this should be called a bug,
I haven't picked up an indication that would lead me to
expect this in the documentation.  I admit that if I had a
deeper understanding of lattice and/or grid, it might be
clearer why...  Here is a toy example illustrating the behavior
(there may be a more efficient way to do this),

ds1 <- data.frame( RR = rep(seq(0, 1, len = 5)^2, 2) +
						rnorm(10, sd = 0.1),
				   LL = rep(10^seq(1, 5), 2),
				   FF = factor(rep(letters[1:2], each = 5))
				   )
ds2 <- data.frame(RR = rep(seq(0, 1, len = 20)^2, 2),
				  LL = rep(10^seq(1, 5, len = 20), 2),
				   FF = factor(rep(letters[1:2], each = 20))
				   )
library(lattice)
xyplot(RR ~ LL | FF, ds1,
		scales = list(x = list(log = TRUE)),
		aspect = "xy",
		subscripts = TRUE,
		ID = ds2$FF,
		panel = function(x, y, subscripts, ID, ...) {
			w <- unique(ds1$FF[subscripts])
			llines(log10(ds2$LL[ID == w]), ds2$RR[ID == w], ...)
			panel.xyplot(x, y, ...)
			}
		)

Note that the x-variable of llines must be logged to plot the correct values
and so the scales argument seems to apply only to the x, y arguments
passed to the panel function.

Thank you.

best,

Ken


-- 
Ken Knoblauch
Inserm U846
Institut Cellule Souche et Cerveau
D?partement Neurosciences Int?gratives
18 avenue du Doyen L?pine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.lyon.inserm.fr/846/english.html

Hi Ken,

Alternatively, you could use ggplot2:

install.packages("ggplot2")
library(ggplot2)

qplot(LL, RR, data=ds1, facets = . ~ FF) + geom_line(data=ds2) + scale_x_log10()

It is very hard to get transformed scales working correctly, and it's
something I had to spend a lot of time on in between ggplot 1 and 2.

Hadley


On 9/3/07, Ken Knoblauch <knoblauch at lyon.inserm.fr>
wrote:
> Hi,
>
> I was taken off guard by the following behavior in a lattice plot.
> I frequently want to add a predicted curve defined at more
> points than in the formula expression of xyplot.  There have
> been numerous examples of how to do this on r-help, but I
> still often struggle to make this work.  I just realized that
> specifying one of the axes on a log scale does not guarantee
> that the added data for a curve will automatically take that
> into account.  I don't know if this should be called a bug,
> I haven't picked up an indication that would lead me to
> expect this in the documentation.  I admit that if I had a
> deeper understanding of lattice and/or grid, it might be
> clearer why...  Here is a toy example illustrating the behavior
> (there may be a more efficient way to do this),
>
> ds1 <- data.frame( RR = rep(seq(0, 1, len = 5)^2, 2) +
>                                                 rnorm(10, sd = 0.1),
>                                    LL = rep(10^seq(1, 5), 2),
>                                    FF = factor(rep(letters[1:2], each = 5))
>                                    )
> ds2 <- data.frame(RR = rep(seq(0, 1, len = 20)^2, 2),
>                                   LL = rep(10^seq(1, 5, len = 20), 2),
>                                    FF = factor(rep(letters[1:2], each =
20))
>                                    )
> library(lattice)
> xyplot(RR ~ LL | FF, ds1,
>                 scales = list(x = list(log = TRUE)),
>                 aspect = "xy",
>                 subscripts = TRUE,
>                 ID = ds2$FF,
>                 panel = function(x, y, subscripts, ID, ...) {
>                         w <- unique(ds1$FF[subscripts])
>                         llines(log10(ds2$LL[ID == w]), ds2$RR[ID == w],
...)
>                         panel.xyplot(x, y, ...)
>                         }
>                 )
>
> Note that the x-variable of llines must be logged to plot the correct
values
> and so the scales argument seems to apply only to the x, y arguments
> passed to the panel function.
>
> Thank you.
>
> best,
>
> Ken
>
>
> --
> Ken Knoblauch
> Inserm U846
> Institut Cellule Souche et Cerveau
> D?partement Neurosciences Int?gratives
> 18 avenue du Doyen L?pine
> 69500 Bron
> France
> tel: +33 (0)4 72 91 34 77
> fax: +33 (0)4 72 91 34 61
> portable: +33 (0)6 84 10 64 10
> http://www.lyon.inserm.fr/846/english.html
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
http://had.co.nz/

On 9/3/07, Ken Knoblauch <knoblauch at lyon.inserm.fr>
wrote:
> Hi,
>
> I was taken off guard by the following behavior in a lattice plot.
> I frequently want to add a predicted curve defined at more
> points than in the formula expression of xyplot.  There have
> been numerous examples of how to do this on r-help, but I
> still often struggle to make this work.  I just realized that
> specifying one of the axes on a log scale does not guarantee
> that the added data for a curve will automatically take that
> into account.  I don't know if this should be called a bug,
More like a possibly desirable feature that's missing.
> I haven't picked up an indication that would lead me to
> expect this in the documentation.
Yes, the documentation is a bit vague. I've changed it to the
following, which is hopefully clearer.

          'log' Controls whether the corresponding variable ('x'
or
               'y') will be log transformed before being passed to the
               panel function.  Defaults to 'FALSE', in which case the
               data are not transformed.  Other possible values are any
               number that works as a base for taking logarithm, 'TRUE'
               (which is equivalent to 10), and '"e"' (for the
natural
               logarithm).  As a side effect, the corresponding axis is
               labeled differently.  Note that this is a transformation
               of the data, not the axes.  Other than the axis
               labeling, using this feature is no different than
               transforming the data in the formula; e.g.,
               'scales=list(x = list(log = 2))' is equivalent to 'y
~
               log2(x)'.

-Deepayan