Re: [R] slplot issue
On 07/18/2010 11:22 PM, Peter Ehlers wrote: ... [Now, I'm having trouble with the pemqzrsTawYY function; can anybody help? :)] Certainly. That is in the WelshRabbit package, which requires the WalesSpeak and dumbBunny packages. Jim __ R-help@r-project.org 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.
Re: [R] slplot issue
Sorry about not answering sooner and providing code. My company mail server died this weekend and I could respond without creating a new account on r-help. The package I'm using is pcaMethods (1.12)(found in the bioconductor packages). The following runs == data(iris) pcIr - pca(iris[,1:4], method=nipals, nPcs=3, cv=q2) slplot(pcIr, sl=as.character(iris[,5]),scoresLoadings=c(TRUE, FALSE)) == and a chart is created. What I would like to do is scale the xlim and ylim such that the x and y scales are the same. I used == slplot(pcIr, sl=as.character(iris[,5]),scoresLoadings=c(TRUE, FALSE), xlim=c(-8,8),ylim=c(-8,8)) == to no avail... Any thoughts? Thank you kindly, -- Shawn Way, PE MECO, Inc. (p) 281-276-7612 (f) 281-313-0248 In which package would one find slplot? It's not in any of the 1800+ packages on my system... Dennis On Sat, Jul 17, 2010 at 1:28 PM, Shawn Way s...@meco.com wrote: In a prior life I was able to use slplot can change the xlim and ylim such that the ellipse was a perfect circle. It seems that the xlim and ylim are no longer supported by the slplot function. Any thoughts on how I can change this? Thank you kindly, nd provide commented, minimal, self-contained, reproducible code. img alt= src=http://www.meco.com/img/meco.gif; /br / a href=http://www.meco.com;WWW.MECO.COM/abr / nbsp; This e-mail is for the use of the intended recipient(s) only. If you have received this e-mail in error, please notify the sender immediately and then delete it. If you are not the intended recipient, you must not use, disclose or distribute this e-mail without the author#39;s prior permission. We have taken precautions to minimize the risk of transmitting software viruses, but we advise you to carry out your own virus checks on any attachment to this message. We cannot accept liability for any loss or damage caused by software viruses. [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] slplot issue
On 2010-07-19 7:50, Shawn Way wrote:
Sorry about not answering sooner and providing code. My company mail
server died this weekend and I could respond without creating a new
account on r-help.
The package I'm using is pcaMethods (1.12)(found in the bioconductor
packages). The following runs
==
data(iris)
pcIr- pca(iris[,1:4], method=nipals, nPcs=3, cv=q2)
slplot(pcIr, sl=as.character(iris[,5]),scoresLoadings=c(TRUE, FALSE))
==
and a chart is created.
What I would like to do is scale the xlim and ylim such that the x and y
scales are the same.
I used
==
slplot(pcIr, sl=as.character(iris[,5]),scoresLoadings=c(TRUE, FALSE),
xlim=c(-8,8),ylim=c(-8,8))
==
to no avail...
Any thoughts?
Shawn,
I can't see how to do what you want with slplot() without
modifying the code. You might have better luck on the
bioconductor list.
But you can always generate the scores plots yourself.
Here are two ways:
## 1. uses base graphics
# make a dataframe of scores
sc - as.data.frame(scores(pcIr))
str(sc)
# set up the plot of PC2 vs PC1; don't plot the points
with(sc, plot(PC1, PC2, type = 'n', xlim = c(-8,8), ylim = c(-8,8)))
# add text at the point locations
with(sc, text(PC1, PC2, iris[,5], cex = 0.5))
# add lines
abline(h = 0, v = 0)
## 2. use lattice
xyplot(PC2 ~ PC1, data=sc, type=n,
xlim = c(-8, 8), ylim = c(-8, 8),
panel=function(x, y, ...){
panel.xyplot(x, y, ...)
panel.text(x, y, labels = iris[,5], cex = 0.5)
panel.abline(h = 0, v = 0)
}
)
-Peter Ehlers
Thank you kindly,
--
Shawn Way, PE
MECO, Inc.
(p) 281-276-7612
(f) 281-313-0248
[]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] slplot issue
It's truly amazing how many people asking for help can't be bothered to report what add-on packages they're using. Shawn's query is a particularly egregious case: slplot is mentioned in pkg:ccmn, which can be found on CRAN, but which depends on pkg:pcaMethods which is on Bioconductor. And pcaMethods has slplot(). Please, folks, do tell us what packages you are using! [Now, I'm having trouble with the pemqzrsTawYY function; can anybody help? :)] -Peter Ehlers On 2010-07-17 16:32, Dennis Murphy wrote: In which package would one find slplot? It's not in any of the 1800+ packages on my system... Dennis __ R-help@r-project.org 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.
[R] slplot issue
In a prior life I was able to use slplot can change the xlim and ylim such that the ellipse was a perfect circle. It seems that the xlim and ylim are no longer supported by the slplot function. Any thoughts on how I can change this? Thank you kindly, -- Shawn Way, PE MECO, Inc. (p) 281-276-7612 (f) 281-313-0248 img alt= src=http://www.meco.com/img/meco.gif; /br / a href=http://www.meco.com;WWW.MECO.COM/abr / nbsp; This e-mail is for the use of the intended recipient(s) only. If you have received this e-mail in error, please notify the sender immediately and then delete it. If you are not the intended recipient, you must not use, disclose or distribute this e-mail without the author#39;s prior permission. We have taken precautions to minimize the risk of transmitting software viruses, but we advise you to carry out your own virus checks on any attachment to this message. We cannot accept liability for any loss or damage caused by software viruses. [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] slplot issue
In which package would one find slplot? It's not in any of the 1800+ packages on my system... Dennis On Sat, Jul 17, 2010 at 1:28 PM, Shawn Way s...@meco.com wrote: In a prior life I was able to use slplot can change the xlim and ylim such that the ellipse was a perfect circle. It seems that the xlim and ylim are no longer supported by the slplot function. Any thoughts on how I can change this? Thank you kindly, -- Shawn Way, PE MECO, Inc. (p) 281-276-7612 (f) 281-313-0248 img alt= src=http://www.meco.com/img/meco.gif; /br / a href=http://www.meco.com;WWW.MECO.COM/abr / nbsp; This e-mail is for the use of the intended recipient(s) only. If you have received this e-mail in error, please notify the sender immediately and then delete it. If you are not the intended recipient, you must not use, disclose or distribute this e-mail without the author#39;s prior permission. We have taken precautions to minimize the risk of transmitting software viruses, but we advise you to carry out your own virus checks on any attachment to this message. We cannot accept liability for any loss or damage caused by software viruses. [[alternative HTML version deleted]] __ R-help@r-project.org 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. [[alternative HTML version deleted]] __ R-help@r-project.org 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.
