[R] Lattice - parallel: xlim and adding lines
Hi, I'm trying to set the minimum and maximum in a parallel plot, but trying xlim=c(-1,1) gives strange results. Am I missing something? The call I give is: parallel(~X[,c(6,9,12,15,18)]|X$ff,X,panel=panel.parallel.new,groups=X$protein,layout=c(3,1),xlim=c(-1,1)) Besides, I would like to add a reference line to the plot, but can't find how to do that. I hope someone can give me a hint or two. Thanks in advance, Tsjerk __ R-help@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
Re: [R] Lattice - parallel: xlim and adding lines
T.A.Wassenaar wrote on 3/29/2005 2:17 PM: Hi, I'm trying to set the minimum and maximum in a parallel plot, but trying xlim=c(-1,1) gives strange results. Am I missing something? The call I give is: parallel(~X[,c(6,9,12,15,18)]|X$ff,X,panel=panel.parallel.new,groups=X$protein,layout=c(3,1),xlim=c(-1,1)) Besides, I would like to add a reference line to the plot, but can't find how to do that. I hope someone can give me a hint or two. Thanks in advance, Tsjerk Tsjerk, I don't think you'll get much help without knowing, first, what strange means, and second, what panel.parallel.new does. And you can always add a reference line by using panel.abline in your panel function. And, from the signature: PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html --sundar __ R-help@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
Re: [R] Lattice - parallel: xlim and adding lines
Hi Sundar, Thanks for the reply. And, oops, the panel.parallel.new shouldn't be in there. That is a revised panel function to color according to a group. As with strange, that would generally be 'not-expected', i.e., in the present case, not having an x-axis running from -1 to 1 for all ranges. I would at least expect to have zero in the middle, but that is not so. Excuse me for not expanding 'strange' previously. I have read the guide.., some while ago. Thanks again, Tsjerk On Tue, 29 Mar 2005 14:42:05 -0600 Sundar Dorai-Raj [EMAIL PROTECTED] wrote: T.A.Wassenaar wrote on 3/29/2005 2:17 PM: Hi, I'm trying to set the minimum and maximum in a parallel plot, but trying xlim=c(-1,1) gives strange results. Am I missing something? The call I give is: parallel(~X[,c(6,9,12,15,18)]|X$ff,X,panel=panel.parallel.new,groups=X$protein,layout=c(3,1),xlim=c(-1,1)) Besides, I would like to add a reference line to the plot, but can't find how to do that. I hope someone can give me a hint or two. Thanks in advance, Tsjerk Tsjerk, I don't think you'll get much help without knowing, first, what strange means, and second, what panel.parallel.new does. And you can always add a reference line by using panel.abline in your panel function. And, from the signature: PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html --sundar __ R-help@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 __ R-help@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
Re: [R] Lattice - parallel: xlim and adding lines
T.A.Wassenaar wrote on 3/29/2005 4:17 PM:
Hi Sundar,
Thanks for the reply. And, oops, the panel.parallel.new shouldn't be in
there. That is a revised panel function to color according to a group.
As with strange, that would generally be 'not-expected', i.e., in the
present case, not having an x-axis running from -1 to 1 for all ranges.
I would at least expect to have zero in the middle, but that is not so.
Excuse me for not expanding 'strange' previously. I have read the
guide.., some while ago.
Thanks again,
Tsjerk
Tsjerk,
From panel.parallel, the x values are being scaled to c(0, 1)
x - (as.numeric(z[subscripts[i], , ]) - llim)/dif
This puts the Min at x == 0 and the Max at x == 1 on the x-axis. If
you want to leave it in the raw scale of the x, you will have to write
your own panel and prepanel function, or simply determine what xlim =
c(-1, 1) is in the scaled coordinates.
E.g.
lin.scale - function(x, a = 0, b = 1, new.x = NULL) {
slope - (b - a)/diff(range(x))
inter - a - slope * min(x)
if(is.null(new.x)) {
inter + slope * x
} else {
inter + slope * new.x
}
}
xlim - lin.scale(range(iris[1:4]), new.x = c(-2, 10))
parallel(~ iris[1:4] | Species, iris, xlim = xlim)
The next question would be how to set the x labels to something other
than Min and Max because (to me) they appear to be hard-coded in
parallel. I will leave that question to Deepayan.
As for adding lines, you will also have to scale your reference line to
the panel units. For my example, each panel has a x range of c(0, 1) and
a y range of c(1, 4). E.g.
my.panel.parallel - function(z, subscripts, col = superpose.line$col,
lwd = superpose.line$lwd,
lty = superpose.line$lty, ...) {
superpose.line - trellis.par.get(superpose.line)
panel.abline(v = 0.5, lwd = 3)
panel.parallel(z, subscripts, col, lwd, lty, ...)
}
HTH,
--sundar
On Tue, 29 Mar 2005 14:42:05 -0600
Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
T.A.Wassenaar wrote on 3/29/2005 2:17 PM:
Hi,
I'm trying to set the minimum and maximum in a parallel plot, but
trying xlim=c(-1,1) gives strange results. Am I missing something?
The call I give is:
parallel(~X[,c(6,9,12,15,18)]|X$ff,X,panel=panel.parallel.new,groups=X$protein,layout=c(3,1),xlim=c(-1,1))
Besides, I would like to add a reference line to the plot, but can't
find how to do that.
I hope someone can give me a hint or two.
Thanks in advance,
Tsjerk
Tsjerk,
I don't think you'll get much help without knowing, first, what
strange means, and second, what panel.parallel.new does. And you
can always add a reference line by using panel.abline in your panel
function.
And, from the signature:
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--sundar
__
R-help@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
__
R-help@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
__
R-help@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
Re: [R] Lattice - parallel: xlim and adding lines
On Tuesday 29 March 2005 17:04, Sundar Dorai-Raj wrote:
T.A.Wassenaar wrote on 3/29/2005 4:17 PM:
Hi Sundar,
Thanks for the reply. And, oops, the panel.parallel.new shouldn't
be in there. That is a revised panel function to color according to
a group. As with strange, that would generally be 'not-expected',
i.e., in the present case, not having an x-axis running from -1 to
1 for all ranges. I would at least expect to have zero in the
middle,
Why??? Why on earth would [-1,1] be something you ``expect'' and [0,1]
be something ``strange''? As far as I can see, neither are documented
(and hence you shouldn't expect anything).
You can of course set 'xlim=c(0,1)', but the better way of doing that
would have been 'scales=list(x = list(axs = i)))'. Unfortunately,
this doesn't currently work in 'parallel', which is a bug.
It's still not very clear to me what you want to.
but that is not so. Excuse me for not expanding 'strange'
previously. I have read the guide.., some while ago.
Thanks again,
Tsjerk
Tsjerk,
From panel.parallel, the x values are being scaled to c(0, 1)
x - (as.numeric(z[subscripts[i], , ]) - llim)/dif
This puts the Min at x == 0 and the Max at x == 1 on the x-axis.
If you want to leave it in the raw scale of the x,
That doesn't really make sense. The whole point of a parallel plot is to
show several variables (with different ranges) in a single plot with a
common axis. This is done by transforming (shifting and linearly
scaling) each variable to have a common range. As such, there's no
'natural choice' for this common range, [0,1] is just as good as any
other [a,b] for -Inf a b Inf.
If you want to do something else, you might as well write your own
prepanel and panel functions.
you will have to
write your own panel and prepanel function, or simply determine what
xlim = c(-1, 1) is in the scaled coordinates.
E.g.
lin.scale - function(x, a = 0, b = 1, new.x = NULL) {
slope - (b - a)/diff(range(x))
inter - a - slope * min(x)
if(is.null(new.x)) {
inter + slope * x
} else {
inter + slope * new.x
}
}
xlim - lin.scale(range(iris[1:4]), new.x = c(-2, 10))
parallel(~ iris[1:4] | Species, iris, xlim = xlim)
The next question would be how to set the x labels to something other
than Min and Max because (to me) they appear to be hard-coded in
parallel. I will leave that question to Deepayan.
My bad (relic of early days). I'll fix it so that they can be overridden
by 'scales'.
As for adding lines, you will also have to scale your reference line
to the panel units. For my example, each panel has a x range of c(0,
1) and a y range of c(1, 4). E.g.
my.panel.parallel - function(z, subscripts, col =
superpose.line$col, lwd = superpose.line$lwd,
lty = superpose.line$lty, ...) {
superpose.line - trellis.par.get(superpose.line)
panel.abline(v = 0.5, lwd = 3)
panel.parallel(z, subscripts, col, lwd, lty, ...)
}
HTH,
--sundar
On Tue, 29 Mar 2005 14:42:05 -0600
Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
T.A.Wassenaar wrote on 3/29/2005 2:17 PM:
Hi,
I'm trying to set the minimum and maximum in a parallel plot, but
trying xlim=c(-1,1) gives strange results. Am I missing
something? The call I give is:
parallel(~X[,c(6,9,12,15,18)]|X$ff,X,panel=panel.parallel.new,gro
ups=X$protein,layout=c(3,1),xlim=c(-1,1))
Besides, I would like to add a reference line to the plot, but
can't find how to do that.
I hope someone can give me a hint or two.
Thanks in advance,
Tsjerk
Tsjerk,
I don't think you'll get much help without knowing, first, what
strange means, and second, what panel.parallel.new does. And
you can always add a reference line by using panel.abline in your
panel function.
And, from the signature:
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--sundar
__
R-help@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
