[R] [lattice::xyplot] Using (panel:.)abline with panel.superpose?
Duncan Mackay
dulcalma at bigpond.com
Thu Oct 8 02:12:41 CEST 2015
Forgot to send to list
-----Original Message-----
From: Duncan Mackay [mailto:dulcalma at bigpond.com]
Sent: Thursday, 8 October 2015 08:44
To: 'Szumiloski, John'
Subject: RE: [R] [lattice::xyplot] Using (panel:.)abline with
panel.superpose?
Hi John
I only got grid lines on your # code 2 with same lattice version on win 7
and blank for the first code
Try
xyplot(Y~X|Trt, data=dat,
groups=Sbj,
type='b',
lty=1,
cex=2,
lwd=3,
scales=list(x=list(at=xgrid), y=list(at=ygrid)),
col=c('red', 'blue'),
pch=c(16,17),
panel= panel.superpose,
panel.groups = function(x,y, ...){
panel.abline(h=ygrid, v=xgrid, col = gray(0.9) )
panel.xyplot(x,y, ...)
}# panel
) # xyplot
It produces grid lines over the lines and points so one way around it is to
use alpha settings.
Not all devices will accept alpha.
xyplot(Y~X|Trt, data=dat,
groups=Sbj,
type='b',
lty=1,
cex=2,
lwd=3,
alpha = 1,
scales=list(x=list(at=xgrid), y=list(at=ygrid)),
col=c('red', 'blue'),
pch=c(16,17),
panel= panel.superpose,
panel.groups = function(x,y,alpha, ...){
panel.abline(h=ygrid, v=xgrid, col=1, alpha = 0.1)
panel.xyplot(x,y, alpha = 1, ...)
}# panel
) # xyplot
If you use par.settings it will give correct colours lines etc to auto key
xyplot(Y~X|Trt, data=dat,
groups=Sbj,
type='b',
par.settings = list(strip.background = list(col = "transparent"),
superpose.line = list(col = c('red', 'blue'),
alpha = 1,
lty=1,lwd=3),
superpose.symbol = list(col=c('red', 'blue'),
alpha = 1,
pch=c(16,17),
cex=2)),
scales=list(x=list(at=xgrid), y=list(at=ygrid)),
auto.key = T,
panel= panel.superpose,
panel.groups = function(x,y,alpha, ...){
panel.abline(h=ygrid, v = xgrid, col=1, alpha = 0.1)
panel.xyplot(x,y, alpha = 1, ...)
}# panel
) # xyplot
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Szumiloski,
John
Sent: Thursday, 8 October 2015 03:40
To: r-help at r-project.org
Subject: [R] [lattice::xyplot] Using (panel:.)abline with panel.superpose?
Dear useRs,
I recently had a query concerning how to customize the graphics parameters
in lattice::xyplot to change not only the color but also the pch symbols,
lty and lwd line parameters, etc., within each grouping variable in the
plot. (https://stat.ethz.ch/pipermail/r-help/2015-July/430285.html). Many
thanks to Mark Leeds who described the solution using panel.superpose as the
panel function and defining a custom panel.groups function using the
subscripts argument.
Here is a crude example. Note how the pch parameter varies with grouping
variable as well as color. I have commented out two lines which are not
important for the example but are for my main question.
#### begin code 1
# R version 3.2.2 release, lattice version 0.20-33, Windows 7.
dat <- data.frame(Trt=rep(c('1','2'), each=10),
Sbj=rep(c('1','2'), each=5),
X=rep(c(0,1,2,3,4), times=4),
Y=c(1,3,3,3,1, 2,4,4,4,2,
3,1,1,1,3, 4,2,2,2,4)
)
xgrid <- seq(0L, 4L)
ygrid <- seq(0L, 5L)
require(lattice)
xyplot(Y ~ X | Trt, data=dat, groups=Sbj, type='b', lty=1, cex=2, lwd=3,
scales=list(x=list(at=xgrid), y=list(at=ygrid)),
### abline=list(h=ygrid, v=xgrid, col=gray(0.8)),
mycol=c('red', 'blue'), mypch=c(16,17),
panel=panel.superpose,
panel.groups=function(x, y, subscripts,
mycol, mypch, col.line, col.symbol, pch,
...) {
### panel.abline(h=ygrid, v=xgrid,
col=gray(0.8))
panel.xyplot(x, y, ...,
pch =
mypch[dat[['Sbj']][subscripts]],
col.symbol =
mycol[dat[['Sbj']][subscripts]],
col.line =
mycol[dat[['Sbj']][subscripts]]
)
} # function
) # xyplot
### end code 1
My question involves the commented out lines. I would like to draw a light
grid in the panels. If I used panel.grid() it would be impossible to get
the gridlines into arbitrary positions, as it seems to pick values similar
to pretty() (I would love to be corrected on this). So we can use an abline
argument to the main xyplot call, or a panel.abline() call in the
panel.groups function.
But either way leads to a problem. The ablines seem to be rerendered for
each level of the grouping variable, thus only the final level is plotted
without being the grid rendered on top of it. Try it by uncommenting either
line.
This is not totally surprising as it does mention somewhere in the
documentation that panel.groups() is called for each value of the grouping
variable. So my question: How do I render the grid just once, before
actually rendering the data, so as to avoid this problem?
I realized a good place to start might be to include panel.abline in the
panel function itself, rather in the panel.groups function called several
times per panel. Thus something like this:
### begin code 2
xyplot(Y~X|Trt, data=dat, groups=Sbj, type='b', lty=1, cex=2, lwd=3,
scales=list(x=list(at=xgrid), y=list(at=ygrid)),
mycol=c('red', 'blue'), mypch=c(16,17),
panel=function(x, y, ...) { ########## <---------------- new
panel function
panel.abline(h=ygrid, v=xgrid, col=gray(0.9))
panel.superpose(x, y, ...)
},
panel.groups=function(x, y, subscripts,
mycol, mypch, col.line, col.symbol, pch,
...) {
panel.xyplot(x, y, ...,
pch =
mypch[dat[['Sbj']][subscripts]],
col.symbol =
mycol[dat[['Sbj']][subscripts]],
col.line =
mycol[dat[['Sbj']][subscripts]]
)
} # function
) # xyplot
### end code 2
Of course this won't work as written, I need to replace the ... arguments
with the right ones. Here is where I am having trouble. I have tried all
kinds of permutations of the mycol etc., xgrid etc., subscripts etc., and
never got the plot to render the ablines once, then the data correctly.
Any assistance greatly appreciated.
John
John Szumiloski, Ph.D.
Principal Scientist, Statistician
Analytical and Bioanalytical Development
NBR105-1-1411
Bristol-Myers Squibb
P.O. Box 191
1 Squibb Drive
New Brunswick, NJ
08903-0191
USA
(732) 227-7167
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