Re: [R] pairs: adjusting margins and labeling axes

[William Michels via R-help]

Hi Michael, is this the direction you'd like to go (simplified)?

?pairs
pairs(iris, log="xy", asp=1, gap=0.1)

--Bill.


On Tue, Jul 19, 2016 at 2:37 PM, Michael Young  wrote:

> I want to make this as easy as possible.  The extra space could just go
> around the plot in the margin area.  I could then use a cropping tool to
> paste the plot into Excel or Word.
>
> I'm not opposed to using another package, but I'd need some kind of
> pre-existing code to tinker with.
>
> On Tue, Jul 19, 2016 at 11:16 AM, Greg Snow <538...@gmail.com> wrote:
>
> > If you want square plots on a rectangular plotting region, then where
> > do you want the extra space to go?
> >
> > One option would be to add outer margins to use up the extra space.
> > The calculations to figure out exactly how much space to put in the
> > outer margins will probably not be trivial.
> >
> > Another option would be to not use `pairs`, but use the `layout`
> > function directly and loops to do your plots (and use the `respect`
> > argument to `layout`).
> >
> > On Tue, Jul 19, 2016 at 11:29 AM, michael young
> >  wrote:
> > > The default shape for this correlation scatterplot is rectangle.  I
> > changed
> > > it to square, but then the x-axis spacing between squares are off.  Is
> > > there an easy way to change x-axis spacing between squares to that of
> the
> > > y-axis spacing size?
> > >
> > > I decided to hide the name values of the diagonal squares.  I want them
> > > along the x and y axis instead, outside of the fixed number scale I
> have.
> > > I haven't seen any online example of 'pairs' with this and all my
> > searches
> > > have yielded nothing.  Any ideas?  Thanks
> > >
> > > par(pty="s")
> > > panel.cor <- function(x, y, digits = 2, prefix="", cex.cor, ...)
> > > {
> > > usr <- par("usr"); on.exit(par(usr))
> > > par(usr = c(0, 1, 0, 1),xlog=FALSE,ylog=FALSE)
> > > # correlation coefficient
> > > r <- cor(x, y)
> > > txt <- format(c(r, 0.123456789), digits = digits)[1]
> > > txt <- paste("r= ", txt, sep = "")
> > > if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
> > > text(0.5, 0.6, txt, cex=cex.cor * r)
> > >
> > > # p-value calculation
> > > p <- cor.test(x, y)$p.value
> > > txt2 <- format(c(p, 0.123456789), digits = digits)[1]
> > > txt2 <- paste("p= ", txt2, sep = "")
> > > if(p<0.01) txt2 <- paste("p= ", "<0.01", sep = "")
> > > text(0.5, 0.4, txt2)
> > > }
> > >
> > > pairs(iris, upper.panel = panel.cor,xlim=c(0.1,10),
> > > ylim=c(0.1,10),log="xy",text.panel = NULL,pch=".")
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > 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.
> >
> >
> >
> > --
> > Gregory (Greg) L. Snow Ph.D.
> > 538...@gmail.com
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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] pairs: adjusting margins and labeling axes

[Michael Young]

I want to make this as easy as possible.  The extra space could just go
around the plot in the margin area.  I could then use a cropping tool to
paste the plot into Excel or Word.

I'm not opposed to using another package, but I'd need some kind of
pre-existing code to tinker with.

On Tue, Jul 19, 2016 at 11:16 AM, Greg Snow <538...@gmail.com> wrote:

> If you want square plots on a rectangular plotting region, then where
> do you want the extra space to go?
>
> One option would be to add outer margins to use up the extra space.
> The calculations to figure out exactly how much space to put in the
> outer margins will probably not be trivial.
>
> Another option would be to not use `pairs`, but use the `layout`
> function directly and loops to do your plots (and use the `respect`
> argument to `layout`).
>
> On Tue, Jul 19, 2016 at 11:29 AM, michael young
>  wrote:
> > The default shape for this correlation scatterplot is rectangle.  I
> changed
> > it to square, but then the x-axis spacing between squares are off.  Is
> > there an easy way to change x-axis spacing between squares to that of the
> > y-axis spacing size?
> >
> > I decided to hide the name values of the diagonal squares.  I want them
> > along the x and y axis instead, outside of the fixed number scale I have.
> > I haven't seen any online example of 'pairs' with this and all my
> searches
> > have yielded nothing.  Any ideas?  Thanks
> >
> > par(pty="s")
> > panel.cor <- function(x, y, digits = 2, prefix="", cex.cor, ...)
> > {
> > usr <- par("usr"); on.exit(par(usr))
> > par(usr = c(0, 1, 0, 1),xlog=FALSE,ylog=FALSE)
> > # correlation coefficient
> > r <- cor(x, y)
> > txt <- format(c(r, 0.123456789), digits = digits)[1]
> > txt <- paste("r= ", txt, sep = "")
> > if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
> > text(0.5, 0.6, txt, cex=cex.cor * r)
> >
> > # p-value calculation
> > p <- cor.test(x, y)$p.value
> > txt2 <- format(c(p, 0.123456789), digits = digits)[1]
> > txt2 <- paste("p= ", txt2, sep = "")
> > if(p<0.01) txt2 <- paste("p= ", "<0.01", sep = "")
> > text(0.5, 0.4, txt2)
> > }
> >
> > pairs(iris, upper.panel = panel.cor,xlim=c(0.1,10),
> > ylim=c(0.1,10),log="xy",text.panel = NULL,pch=".")
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
>
>
> --
> Gregory (Greg) L. Snow Ph.D.
> 538...@gmail.com
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] pairs: adjusting margins and labeling axes

[Duncan Mackay]

Hi
Will doing in lattice suite

>From  https://stat.ethz.ch/pipermail/r-help/2007-October/142116.html and
https://stat.ethz.ch/pipermail/r-help/2007-October/142124.html]
This is a direct cut and paste from the last url to give you an idea of
Deepayan Sarkar's script

library(lattice)

panel.corval2 <- function(x, y, digits=2, prefix="", cex.cor, ...)
{
require(grid)
r <- abs(cor(x, y, use = "complete.obs"))
txt <- format(c(r, 0.123456789), digits=digits)[1]
txt <- paste(prefix, txt, sep="")
if (missing(cex.cor)) cex.cor <- 10 / nchar(txt)
grid.text(txt, 0.5, 0.5, gp = gpar(cex = cex.cor))
}

splom(iris[1:4], groups = iris$Species, pch = 16,
  lower.panel = function(...) {
  panel.xyplot(...)
  panel.loess(..., col = 1, lwd = 3)
  },
  upper.panel = panel.corval2)


Regards

Duncan

Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of michael
young
Sent: Wednesday, 20 July 2016 03:30
To: r-help@r-project.org
Subject: [R] pairs: adjusting margins and labeling axes

The default shape for this correlation scatterplot is rectangle.  I changed
it to square, but then the x-axis spacing between squares are off.  Is
there an easy way to change x-axis spacing between squares to that of the
y-axis spacing size?

I decided to hide the name values of the diagonal squares.  I want them
along the x and y axis instead, outside of the fixed number scale I have.
I haven't seen any online example of 'pairs' with this and all my searches
have yielded nothing.  Any ideas?  Thanks

par(pty="s")
panel.cor <- function(x, y, digits = 2, prefix="", cex.cor, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1),xlog=FALSE,ylog=FALSE)
# correlation coefficient
r <- cor(x, y)
txt <- format(c(r, 0.123456789), digits = digits)[1]
txt <- paste("r= ", txt, sep = "")
if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
text(0.5, 0.6, txt, cex=cex.cor * r)

# p-value calculation
p <- cor.test(x, y)$p.value
txt2 <- format(c(p, 0.123456789), digits = digits)[1]
txt2 <- paste("p= ", txt2, sep = "")
if(p<0.01) txt2 <- paste("p= ", "<0.01", sep = "")
text(0.5, 0.4, txt2)
}

pairs(iris, upper.panel = panel.cor,xlim=c(0.1,10),
ylim=c(0.1,10),log="xy",text.panel = NULL,pch=".")

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] pairs: adjusting margins and labeling axes

[Greg Snow]

If you want square plots on a rectangular plotting region, then where
do you want the extra space to go?

One option would be to add outer margins to use up the extra space.
The calculations to figure out exactly how much space to put in the
outer margins will probably not be trivial.

Another option would be to not use `pairs`, but use the `layout`
function directly and loops to do your plots (and use the `respect`
argument to `layout`).

On Tue, Jul 19, 2016 at 11:29 AM, michael young
 wrote:
> The default shape for this correlation scatterplot is rectangle.  I changed
> it to square, but then the x-axis spacing between squares are off.  Is
> there an easy way to change x-axis spacing between squares to that of the
> y-axis spacing size?
>
> I decided to hide the name values of the diagonal squares.  I want them
> along the x and y axis instead, outside of the fixed number scale I have.
> I haven't seen any online example of 'pairs' with this and all my searches
> have yielded nothing.  Any ideas?  Thanks
>
> par(pty="s")
> panel.cor <- function(x, y, digits = 2, prefix="", cex.cor, ...)
> {
> usr <- par("usr"); on.exit(par(usr))
> par(usr = c(0, 1, 0, 1),xlog=FALSE,ylog=FALSE)
> # correlation coefficient
> r <- cor(x, y)
> txt <- format(c(r, 0.123456789), digits = digits)[1]
> txt <- paste("r= ", txt, sep = "")
> if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
> text(0.5, 0.6, txt, cex=cex.cor * r)
>
> # p-value calculation
> p <- cor.test(x, y)$p.value
> txt2 <- format(c(p, 0.123456789), digits = digits)[1]
> txt2 <- paste("p= ", txt2, sep = "")
> if(p<0.01) txt2 <- paste("p= ", "<0.01", sep = "")
> text(0.5, 0.4, txt2)
> }
>
> pairs(iris, upper.panel = panel.cor,xlim=c(0.1,10),
> ylim=c(0.1,10),log="xy",text.panel = NULL,pch=".")
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.



-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] pairs: adjusting margins and labeling axes

[michael young]

The default shape for this correlation scatterplot is rectangle.  I changed
it to square, but then the x-axis spacing between squares are off.  Is
there an easy way to change x-axis spacing between squares to that of the
y-axis spacing size?

I decided to hide the name values of the diagonal squares.  I want them
along the x and y axis instead, outside of the fixed number scale I have.
I haven't seen any online example of 'pairs' with this and all my searches
have yielded nothing.  Any ideas?  Thanks

par(pty="s")
panel.cor <- function(x, y, digits = 2, prefix="", cex.cor, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1),xlog=FALSE,ylog=FALSE)
# correlation coefficient
r <- cor(x, y)
txt <- format(c(r, 0.123456789), digits = digits)[1]
txt <- paste("r= ", txt, sep = "")
if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
text(0.5, 0.6, txt, cex=cex.cor * r)

# p-value calculation
p <- cor.test(x, y)$p.value
txt2 <- format(c(p, 0.123456789), digits = digits)[1]
txt2 <- paste("p= ", txt2, sep = "")
if(p<0.01) txt2 <- paste("p= ", "<0.01", sep = "")
text(0.5, 0.4, txt2)
}

pairs(iris, upper.panel = panel.cor,xlim=c(0.1,10),
ylim=c(0.1,10),log="xy",text.panel = NULL,pch=".")

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] pairs plot

[Witold E Wolski]

my data are matrix with 3 numeric columns.

would like to have pairs plot
with scatterplots in the upper
with hist at the diag
and with correlation at the lower.

actually default pairs does almost what I want but looks semi awesome.
Especially, i didn't find out how to remove the axes from the lower
part where I do only want to display the numeric values correlations
there and somehow axes don't fit.

Hence I am looking at ggpairs from GGally
and calling it without parameters looks almost perfect :
but I cant find out how they got the Corr: in the upper, so I can't
put it in the lower,
and I do not know how to put the hist in the diag.

please help






-- 
Witold Eryk Wolski

__
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] pairs plot

[Jim Lemon]

On 10/11/2013 02:01 AM, Witold E Wolski wrote:

my data are matrix with 3 numeric columns.

would like to have pairs plot
with scatterplots in the upper
with hist at the diag
and with correlation at the lower.

actually default pairs does almost what I want but looks semi awesome.
Especially, i didn't find out how to remove the axes from the lower
part where I do only want to display the numeric values correlations
there and somehow axes don't fit.

Hence I am looking at ggpairs from GGally
and calling it without parameters looks almost perfect :
but I cant find out how they got the Corr: in the upper, so I can't
put it in the lower,
and I do not know how to put the hist in the diag.


Hi Witold,
The example below is roughly what you want, I think. This could be 
wrapped up in a function similar to pairs and I might do this in 
future if I get the time.


wwdat-data.frame(a=seq(1,5,length.out=20)+rnorm(20),
 b=seq(1,4,length.out=20)+rnorm(20),c=rnorm(20))
require(plotrix)
panes(matrix(1:9,nrow=3,byrow=TRUE),c(1.2,1,1.2),c(1.2,1,1.2))
# plot 1
par(mar=c(0,3,3,0))
hist(wwdat$a,xaxt=n,xlab=,ylab=,main=)
box()
# plot 2
par(mar=c(0,0,3,0))
plot(wwdat$a,wwdat$b,xaxt=n,yaxt=n,xlab=,ylab=)
axis(3)
# plot 3
par(mar=c(0,0,3,3))
plot(wwdat$a,wwdat$c,xaxt=n,yaxt=n,xlab=,ylab=)
axis(3)
axis(4)
# plot 4
par(mar=c(0,3,0,0))
plot(0,0,xlim=c(-1,1),ylim=c(-1,1),xaxt=n,yaxt=n,xlab=,ylab=,type=n)
text(0,0,round(cor(wwdat$a,wwdat$b),2),cex=2.5)
# plot 5
par(mar=c(0,0,0,0))
hist(wwdat$b,xaxt=n,yaxt=n,xlab=,ylab=,main=)
# plot 6
par(mar=c(0,0,0,3))
plot(wwdat$b,wwdat$c,xaxt=n,yaxt=n,xlab=,ylab=)
axis(4)
# plot 7
par(mar=c(3,3,0,0))
plot(0,0,xlim=c(-1,1),ylim=c(-1,1),xaxt=n,yaxt=n,xlab=,ylab=,type=n)
text(0,0,round(cor(wwdat$c,wwdat$a),2),cex=2.5)
# plot 8
par(mar=c(3,0,0,0))
plot(0,0,xlim=c(-1,1),ylim=c(-1,1),xaxt=n,yaxt=n,xlab=,ylab=,type=n)
text(0,0,round(cor(wwdat$c,wwdat$b),2),cex=2.5)
# plot 9
par(mar=c(3,0,0,3))
hist(wwdat$c,xaxt=n,yaxt=n,xlab=,ylab=,main=)
axis(4)
box()

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.

[R] pairs(X,Y) analog of cor(X,Y)?

[Michael Friendly]

With a data frame containing some X  Y variables I can get the between 
set correlations

with cor(X,Y):

 cor(NLSY[,1:2], NLSY[3:6])
  antisochyperact income  educ
math  0.043381307 -0.07581733 0.25487753 0.2876875
read -0.003735785 -0.07555683 0.09114299 0.1884101

Is there somewhere an analog of pairs(X,Y) that will produce the pairwise
plots of each X against each Y?
The formula method for pairs() is for a one-sided formula.  As a 
formula, I'm looking

for something like

pairs(math + read ~ antisoc +hyperact + income +  educ, data=NLSY)

lattice::xyplot has an extended formula interface, but interprets '+' to 
mean

superposition.

--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.  Chair, Quantitative Methods
York University  Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

__
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] pairs(X,Y) analog of cor(X,Y)?

[Greg Snow]

There is the pairs2 function in the TeachingDemos package that works like
cor(x,y) where you give it 2 matricies/data frames and it gives the
pairwise plots between the 2 groups.  There is currently not a formula
interface.


On Fri, Mar 29, 2013 at 12:16 PM, Michael Friendly frien...@yorku.cawrote:

 With a data frame containing some X  Y variables I can get the between
 set correlations
 with cor(X,Y):

  cor(NLSY[,1:2], NLSY[3:6])
   antisochyperact income  educ
 math  0.043381307 -0.07581733 0.25487753 0.2876875
 read -0.003735785 -0.07555683 0.09114299 0.1884101

 Is there somewhere an analog of pairs(X,Y) that will produce the pairwise
 plots of each X against each Y?
 The formula method for pairs() is for a one-sided formula.  As a formula,
 I'm looking
 for something like

 pairs(math + read ~ antisoc +hyperact + income +  educ, data=NLSY)

 lattice::xyplot has an extended formula interface, but interprets '+' to
 mean
 superposition.

 --
 Michael Friendly Email: friendly AT yorku DOT ca
 Professor, Psychology Dept.  Chair, Quantitative Methods
 York University  Voice: 416 736-2100 x66249 Fax: 416 736-5814
 4700 Keele StreetWeb:   http://www.datavis.ca
 Toronto, ONT  M3J 1P3 CANADA

 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/**
 posting-guide.html http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

[[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] pairs(), expression in label and color in text.panel

[Uwe Ligges]

On 24.11.2011 15:59, Johannes Radinger wrote:

Hello,

I'd like to add custom labels to my pair() plot. These
labels include math expression but they aren't correctly
displayed...


Looks fine for me in R-2.14.0 on the windows() device (alpha, text, 
beta). (Both version and device you used are unspecified)




Further, I want that the boxes for the text.panel (diagonal)
have an other background color (grey80). Is that generally
possible? If yes how do I have to set it?

What I've so far is:


panel.cor- function(x, y, digits=2, prefix=, cex.cor)
{
usr- par(usr); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r- abs(cor(x, y))
txt- format(c(r, 0.123456789), digits=digits)[1]
txt- paste(prefix, txt, sep=)
if(missing(cex.cor)) cex- 0.5/strwidth(txt)

test- cor.test(x,y)
# borrowed from printCoefmat
Signif- symnum(test$p.value, corr = FALSE, na = FALSE,
cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
symbols = c(***, **, *, .,  ))

text(0.5, 0.5, paste(txt,Signif), cex = 2)
}

#correlation pair plot
pairs(df, labels=c(expression(alpha),text,expression(beta)), 
lower.panel=panel.smooth, upper.panel=panel.cor)



Not easily without changing the original code, I think, but you can cheat:

pairs(iris, labels = expression(alpha, text, beta),
lower.panel=panel.smooth, upper.panel=panel.cor,
diag.panel = function(...)
rect(par(usr)[1], par(usr)[3],
 par(usr)[2], par(usr)[4], col=grey80)
)


Best,
Uwe Ligges




Maybe someone knows how to do that and can give some hints...

/Johannes

--

__
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-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] pairs(), expression in label and color in text.panel

[Johannes Radinger]

Hello,

I'd like to add custom labels to my pair() plot. These
labels include math expression but they aren't correctly
displayed...

Further, I want that the boxes for the text.panel (diagonal)
have an other background color (grey80). Is that generally 
possible? If yes how do I have to set it?

What I've so far is:


panel.cor - function(x, y, digits=2, prefix=, cex.cor)
{
usr - par(usr); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r - abs(cor(x, y))
txt - format(c(r, 0.123456789), digits=digits)[1]
txt - paste(prefix, txt, sep=)
if(missing(cex.cor)) cex - 0.5/strwidth(txt)

test - cor.test(x,y)
# borrowed from printCoefmat
Signif - symnum(test$p.value, corr = FALSE, na = FALSE,
cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
symbols = c(***, **, *, .,  ))

text(0.5, 0.5, paste(txt,Signif), cex = 2)
}

#correlation pair plot
pairs(df, labels=c(expression(alpha),text,expression(beta)), 
lower.panel=panel.smooth, upper.panel=panel.cor)


Maybe someone knows how to do that and can give some hints...

/Johannes

--

__
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] pairs(), no axis labels/values for upper panel?

[B77S]

Steffen, 

Did you ever have luck getting rid of the tick marks?...  
I like your idea and have modified it, but yes, the tick marks need to go.



Steffen Fleischer wrote:
 
 Dear all,
 
 I want to draw a graph that contains the scatterplot matrix in the lower
 panel and coefficients in the upper panel. I used and adapted the example
 for the function pairs but cannot figure out how to get no values and
 ticks in the upper panel (the values should only be in the lower panel).
 The upper panel looks odd to me this way. Any hints?
 
 Thanks in advance
 Steffen
 
 
 Here is an example what the graph looks like:
 #
 data(mtcars)
 panel.cor - function(a, b, digits=2,  ...)
  {
  
   usr - par(usr); on.exit(par(usr))
  par(usr = c(0, 1, 0, 1))
  x-cbind(a,b)
  x-na.omit(x)
  n - nrow(x)
  pp - c(0.025, 0.975)
  corx - cor(x,method=s)[1, 2]
  CI-c(tanh(atanh(corx) + qnorm(pp)/sqrt((n - 3)/1.06)))
  txt1 - paste(rho =,format(c(corx, 0.123456789),
 digits=digits)[1])
  txt2-paste((,format(c(CI,0.123456789)[1],digits=digits),;
 ,format(c(CI,0.123456789)[2],digits=digits),),sep=)
  txt3-paste(N =,round(n,0))
  txt - paste(txt1,\n,95%KI ,txt2,\n,txt3, sep=)
  text(0.5, 0.5, txt,cex=.8)
  }

 diag.cor-function(a,b, ...)
 {
 usr - par(usr); on.exit(par(usr))
 par(usr = c(0, 1, 0,1))
 rect(0,0,1,1,col=grey)
  }
 
 pairs(mtcars[1:4],upper.panel=panel.cor,diag.panel=diag.cor,label.pos=0.5)
 #
 
 __
 R-help@ 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.
 


--
View this message in context: 
http://r.789695.n4.nabble.com/pairs-no-axis-labels-values-for-upper-panel-tp3234437p4075283.html
Sent from the R help mailing list archive at Nabble.com.

__
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] pairs(), no axis labels/values for upper panel?

[Steffen Fleischer]

Dear all,

I want to draw a graph that contains the scatterplot matrix in the lower panel 
and coefficients in the upper panel. I used and adapted the example for the 
function pairs but cannot figure out how to get no values and ticks in the 
upper panel (the values should only be in the lower panel). The upper panel 
looks odd to me this way. Any hints?

Thanks in advance
Steffen


Here is an example what the graph looks like:
#
data(mtcars)
panel.cor - function(a, b, digits=2,  ...)
 {
 
usr - par(usr); on.exit(par(usr))
 par(usr = c(0, 1, 0, 1))
 x-cbind(a,b)
 x-na.omit(x)
 n - nrow(x)
 pp - c(0.025, 0.975)
 corx - cor(x,method=s)[1, 2]
 CI-c(tanh(atanh(corx) + qnorm(pp)/sqrt((n - 3)/1.06)))
 txt1 - paste(rho =,format(c(corx, 0.123456789), digits=digits)[1])
 txt2-paste((,format(c(CI,0.123456789)[1],digits=digits),; 
,format(c(CI,0.123456789)[2],digits=digits),),sep=)
 txt3-paste(N =,round(n,0))
 txt - paste(txt1,\n,95%KI ,txt2,\n,txt3, sep=)
 text(0.5, 0.5, txt,cex=.8)
 }
 
diag.cor-function(a,b, ...)
{
usr - par(usr); on.exit(par(usr))
par(usr = c(0, 1, 0,1))
rect(0,0,1,1,col=grey)
 }

pairs(mtcars[1:4],upper.panel=panel.cor,diag.panel=diag.cor,label.pos=0.5)
#

__
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] pairs and mfrow

[Mike Harwood]

Is there an alternative to par(mfrow=c(2,1)) to get stacked scatterplot
matrixes generated with pairs?

I am using version 2.11.1 on Windows XP.  The logic I am using follows, and
the second pairs plot replaces the first plot in the current graphics
device, which is not what I expected (or desired).

par(mfrow=c(2,1))
pairs(b2007, main=6/2000 - 12/2006)
pairs(a2007, main=1/2007 - 06/2009)

Thanks in advance!

Mike

[[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] pairs and mfrow

[Greg Snow]

Why do you want 2 pairs plots on the same device?  There may be a better 
approach to what you want to do.

You could use splom from the lattice package along with the print.trellis 
function to put 2 on the same page.

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Mike Harwood
 Sent: Monday, September 27, 2010 6:51 AM
 To: r-help@r-project.org
 Subject: [R] pairs and mfrow
 
 Is there an alternative to par(mfrow=c(2,1)) to get stacked scatterplot
 matrixes generated with pairs?
 
 I am using version 2.11.1 on Windows XP.  The logic I am using follows,
 and
 the second pairs plot replaces the first plot in the current graphics
 device, which is not what I expected (or desired).
 
 par(mfrow=c(2,1))
 pairs(b2007, main=6/2000 - 12/2006)
 pairs(a2007, main=1/2007 - 06/2009)
 
 Thanks in advance!
 
 Mike
 
   [[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.

__
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] pairs and panel.smooth for two groups

[Marie-Pierre Sylvestre]

Hi,
I have modified the USJudgeRatings data (available in R)  to
illustrate my question.

# Use the first 4 variables of USJudgeRatings and add a group variable
with two levels
USJudgeRatings - USJudgeRatings[,1:4]
USJudgeRatings$group - factor(c(rep(1, 22), rep(0, 21)))

# I can draw a pairs graph where members of each group are drawn in
different colors:

pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch =
c(21,3)[USJudgeRatings$group])

# I would also like to add a smooth line to each subplot like
pairs(USJudgeRatings[,1:4], panel=panel.smooth)

# but I want the smooth to be done for each of the group, i.e. I want
two smooths per subplot.

# this creates only one smooth
pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch =
c(21,3)[USJudgeRatings$group], panel = panel.smooth)

# I understand that panel.smooth is a function that is called for each
subplot. I don't know how to tell it to do a smooth for each of my
group in each of the subplot.

Any help would be appreciated!

Best,

Marie-Pierre

__
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] pairs and panel.smooth for two groups

[Greg Snow]

This is fairly simple using lattice graphics:

USJudgeRatings - USJudgeRatings[,1:4]
USJudgeRatings$group - factor(c(rep(1, 22), rep(0, 21)))

library(lattice)
splom( ~USJudgeRatings[,1:4], groups=group, data=USJudgeRatings,
type=c('p','smooth'))


The ggplot2 package probably makes this easy as well (but I am still learning 
that).

If you really need to use the pairs function then you will need to create your 
own panel function (which could call panel.smooth).

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Marie-Pierre Sylvestre
 Sent: Wednesday, September 08, 2010 8:03 AM
 To: r-help@r-project.org
 Subject: [R] pairs and panel.smooth for two groups
 
 Hi,
 I have modified the USJudgeRatings data (available in R)  to
 illustrate my question.
 
 # Use the first 4 variables of USJudgeRatings and add a group variable
 with two levels
 USJudgeRatings - USJudgeRatings[,1:4]
 USJudgeRatings$group - factor(c(rep(1, 22), rep(0, 21)))
 
 # I can draw a pairs graph where members of each group are drawn in
 different colors:
 
 pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch =
 c(21,3)[USJudgeRatings$group])
 
 # I would also like to add a smooth line to each subplot like
 pairs(USJudgeRatings[,1:4], panel=panel.smooth)
 
 # but I want the smooth to be done for each of the group, i.e. I want
 two smooths per subplot.
 
 # this creates only one smooth
 pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch =
 c(21,3)[USJudgeRatings$group], panel = panel.smooth)
 
 # I understand that panel.smooth is a function that is called for each
 subplot. I don't know how to tell it to do a smooth for each of my
 group in each of the subplot.
 
 Any help would be appreciated!
 
 Best,
 
 Marie-Pierre
 
 __
 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-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] pairs with same xlim and ylim scale

[Dejian Zhao]

Well done!  I was totally misled and trapped by the error message. 
Acturally the absence of 1.00 in the upper panel is an implicit 
indication that error occurred there.


On 2010-9-3 13:02, Shi, Tao wrote:

Hi Dejian,

Thanks for the reply!

I finally found the problem.  It is actually in the panel.cor function.
Adding ... in the function and text call fixed everything.


Best,

...Tao




- Original Message 
   

From: Dejian Zhaodejian.z...@gmail.com
To: r-help@r-project.org
Sent: Thu, September 2, 2010 7:57:55 PM
Subject: Re: [R] pairs with same xlim and ylim scale

When pairs draws plots, lower.panel invokes f.xy. Maybe there is
something in f.xy incompatible with pairs. You can read the code of
pairs to see what happens.

pairs has two methods, as you can see  in the help message (?pairs).
According to your code, pairs is supposed to  invoke Default S3 method.
methods(pairs)
[1] pairs.default   pairs.formula*
 Non-visible functions are  asterisked
Therefore, you should check the code of the function  pairs.default to
see how error occurs. Just type pairs.default at the R  command prompt
and enter, you can get the source code of  pairs.default.



On 2010-9-2 15:15, Shi, Tao wrote:
 

Hi  Dejian,

You're right on this!  Do you know how to pass  those two argument into
lower.panel?  Thanks!

  ...Tao



From:  Dejian Zhaozha...@ioz.ac.cn
To:r-help@r-project.org
Sent: Tue,  August 31, 2010 6:10:16 PM
Subject: Re: [R] pairs with same xlim and  ylim scale

I think you have successfully passed the xlim and  ylim into the
function pairs1. Compare the two graphs produced by the  codes you
provided, you can find the xlim and ylim in the second graph  have been
reset to the assigned value. It seems that the program halted  in
producing the second plot after adding xlim and ylim. According to  the
error message, the two added parameters were not used in  lower.panel, or
the customized function f.xy.

On  2010-9-1 2:26, Shi, Tao wrote:

   

Hi  list,

I have a function which basically is a wrapper of  pairs with some useful
 

panel
 

functions.  However, I'm having  trouble to pass the xlim and ylim into
 

the
 

function so the x and  y axes are in the same scale and 45 degree lines are
exactly  diagonal.   I've looked at some old posts, they didn't help much.
 

I
 


 

[[elided Yahoo spam]]

   

Thanks!

  ...Tao


pairs1- function(x, ...)  {
   f.xy- function(x, y, ...)  {
   points(x, y,  ...)
   abline(0, 1,  col = 2)
   }

panel.cor- function(x, y, digits=2, prefix=, cex.cor)  {
usr- par(usr);  on.exit(par(usr))
par(usr =  c(0, 1, 0, 1))
r-  abs(cor(x, y, method=p, use=pairwise.complete.obs))
 txt- format(c(r, 0.123456789),  digits=digits)[1]
txt-  paste(prefix, txt, sep=)
 if(missing(cex.cor)) cex- 0.8/strwidth(txt)
 text(0.5, 0.5, txt, cex = cex * r)
 }

 panel.hist- function(x, ...) {
 usr- par(usr); on.exit(par(usr))
 par(usr = c(usr[1:2], 0, 1.5) )
 h- hist(x, plot = FALSE)
 breaks- h$breaks; nB-  length(breaks)
y-  h$counts; y- y/max(y)
 rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
 }

   pairs(x,  lower.panel=f.xy, upper.panel=panel.cor,
 

diag.panel=panel.hist,
 

  ...)
}



 

x- rnorm(100, sd=0.2)
x- cbind(x=x-0.1,  y=x+0.1)
pairs1(x)
pairs1(x, xlim=c(-1,1),  ylim=c(-1,1))


   

Error in lower.panel(...) :
 unused  argument(s) (xlim = c(-1, 1), ylim = c(-1,  1))



   [[alternative HTML version deleted]]

  __
R-help@r-project.org  mailing  list
https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting
 

guidehttp://www.R-project.org/posting-guide.html
 

and provide  commented, minimal, self-contained, reproducible  code.


 

  __
R-help@r-project.org  mailing  list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE  do read the posting guidehttp://www.R-project.org/posting-guide.html
and  provide commented, minimal, self-contained, reproducible code.

  __
R-help@r-project.org  mailing  list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE  do read the posting guidehttp://www.R-project.org/posting-guide.html
and  provide commented, minimal, self-contained, reproducible  code.

   

__
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-help@r-project.org mailing list
https

Re: [R] pairs with same xlim and ylim scale

[Shi, Tao]

Hi Dejian,

You're right on this!  Do you know how to pass those two argument into 
lower.panel?  Thanks!

...Tao



From: Dejian Zhao zha...@ioz.ac.cn
To: r-help@r-project.org
Sent: Tue, August 31, 2010 6:10:16 PM
Subject: Re: [R] pairs with same xlim and ylim scale

I think you have successfully passed the xlim and ylim into the 
function pairs1. Compare the two graphs produced by the codes you 
provided, you can find the xlim and ylim in the second graph have been 
reset to the assigned value. It seems that the program halted in 
producing the second plot after adding xlim and ylim. According to the 
error message, the two added parameters were not used in lower.panel, or 
the customized function f.xy.

On 2010-9-1 2:26, Shi, Tao wrote:
 Hi list,

 I have a function which basically is a wrapper of pairs with some useful panel
 functions.  However, I'm having trouble to pass the xlim and ylim into the
 function so the x and y axes are in the same scale and 45 degree lines are
 exactly diagonal.   I've looked at some old posts, they didn't help much.  I
[[elided Yahoo spam]]

 Thanks!

 ...Tao


 pairs1- function(x, ...) {
  f.xy- function(x, y, ...) {
  points(x, y, ...)
  abline(0, 1, col = 2)
  }

  panel.cor- function(x, y, digits=2, prefix=, cex.cor) {
   usr- par(usr); on.exit(par(usr))
   par(usr = c(0, 1, 0, 1))
   r- abs(cor(x, y, method=p, use=pairwise.complete.obs))
   txt- format(c(r, 0.123456789), digits=digits)[1]
   txt- paste(prefix, txt, sep=)
   if(missing(cex.cor)) cex- 0.8/strwidth(txt)
   text(0.5, 0.5, txt, cex = cex * r)
   }

   panel.hist- function(x, ...) {
   usr- par(usr); on.exit(par(usr))
   par(usr = c(usr[1:2], 0, 1.5) )
   h- hist(x, plot = FALSE)
   breaks- h$breaks; nB- length(breaks)
   y- h$counts; y- y/max(y)
   rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
   }

  pairs(x, lower.panel=f.xy, upper.panel=panel.cor, diag.panel=panel.hist,
 ...)
 }


 x- rnorm(100, sd=0.2)
 x- cbind(x=x-0.1, y=x+0.1)
 pairs1(x)
 pairs1(x, xlim=c(-1,1), ylim=c(-1,1))
  
 Error in lower.panel(...) :
unused argument(s) (xlim = c(-1, 1), ylim = c(-1, 1))



 [[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.


__
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-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] pairs with same xlim and ylim scale

[Dejian Zhao]

When pairs draws plots, lower.panel invokes f.xy. Maybe there is 
something in f.xy incompatible with pairs. You can read the code of 
pairs to see what happens.


pairs has two methods, as you can see in the help message (?pairs). 
According to your code, pairs is supposed to invoke Default S3 method.

 methods(pairs)
[1] pairs.default  pairs.formula*
   Non-visible functions are asterisked
Therefore, you should check the code of the function pairs.default to 
see how error occurs. Just type pairs.default at the R command prompt 
and enter, you can get the source code of pairs.default.




On 2010-9-2 15:15, Shi, Tao wrote:

Hi Dejian,

You're right on this!  Do you know how to pass those two argument into
lower.panel?  Thanks!

...Tao



From: Dejian Zhaozha...@ioz.ac.cn
To:r-help@r-project.org
Sent: Tue, August 31, 2010 6:10:16 PM
Subject: Re: [R] pairs with same xlim and ylim scale

I think you have successfully passed the xlim and ylim into the
function pairs1. Compare the two graphs produced by the codes you
provided, you can find the xlim and ylim in the second graph have been
reset to the assigned value. It seems that the program halted in
producing the second plot after adding xlim and ylim. According to the
error message, the two added parameters were not used in lower.panel, or
the customized function f.xy.

On 2010-9-1 2:26, Shi, Tao wrote:
   

Hi list,

I have a function which basically is a wrapper of pairs with some useful panel
functions.  However, I'm having trouble to pass the xlim and ylim into the
function so the x and y axes are in the same scale and 45 degree lines are
exactly diagonal.   I've looked at some old posts, they didn't help much.  I
 

[[elided Yahoo spam]]
   

Thanks!

...Tao


pairs1- function(x, ...) {
  f.xy- function(x, y, ...) {
  points(x, y, ...)
  abline(0, 1, col = 2)
  }

  panel.cor- function(x, y, digits=2, prefix=, cex.cor) {
   usr- par(usr); on.exit(par(usr))
   par(usr = c(0, 1, 0, 1))
   r- abs(cor(x, y, method=p, use=pairwise.complete.obs))
   txt- format(c(r, 0.123456789), digits=digits)[1]
   txt- paste(prefix, txt, sep=)
   if(missing(cex.cor)) cex- 0.8/strwidth(txt)
   text(0.5, 0.5, txt, cex = cex * r)
   }

   panel.hist- function(x, ...) {
   usr- par(usr); on.exit(par(usr))
   par(usr = c(usr[1:2], 0, 1.5) )
   h- hist(x, plot = FALSE)
   breaks- h$breaks; nB- length(breaks)
   y- h$counts; y- y/max(y)
   rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
   }

  pairs(x, lower.panel=f.xy, upper.panel=panel.cor, diag.panel=panel.hist,
...)
}


 

x- rnorm(100, sd=0.2)
x- cbind(x=x-0.1, y=x+0.1)
pairs1(x)
pairs1(x, xlim=c(-1,1), ylim=c(-1,1))

   

Error in lower.panel(...) :
unused argument(s) (xlim = c(-1, 1), ylim = c(-1, 1))



 [[alternative HTML version deleted]]

__
R-help@r-project.org  mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

 

__
R-help@r-project.org  mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org  mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




__
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] pairs with same xlim and ylim scale

[Shi, Tao]

Hi list,

I have a function which basically is a wrapper of pairs with some useful panel 
functions.  However, I'm having trouble to pass the xlim and ylim into the 
function so the x and y axes are in the same scale and 45 degree lines are 
exactly diagonal.   I've looked at some old posts, they didn't help much.  I 
think this is b/c I have multiple panel functions.  Help!

Thanks!

...Tao


pairs1 - function(x, ...) {
f.xy - function(x, y, ...) {
points(x, y, ...)
abline(0, 1, col = 2)
}

panel.cor - function(x, y, digits=2, prefix=, cex.cor) {
 usr - par(usr); on.exit(par(usr))
 par(usr = c(0, 1, 0, 1))
 r - abs(cor(x, y, method=p, use=pairwise.complete.obs))
 txt - format(c(r, 0.123456789), digits=digits)[1]
 txt - paste(prefix, txt, sep=)
 if(missing(cex.cor)) cex - 0.8/strwidth(txt)
 text(0.5, 0.5, txt, cex = cex * r)
 }

 panel.hist - function(x, ...) {
 usr - par(usr); on.exit(par(usr))
 par(usr = c(usr[1:2], 0, 1.5) )
 h - hist(x, plot = FALSE)
 breaks - h$breaks; nB - length(breaks)
 y - h$counts; y - y/max(y)
 rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
 }

pairs(x, lower.panel=f.xy, upper.panel=panel.cor, diag.panel=panel.hist, 
...)
}

 x - rnorm(100, sd=0.2)
 x - cbind(x=x-0.1, y=x+0.1) 
 pairs1(x)
 pairs1(x, xlim=c(-1,1), ylim=c(-1,1))
Error in lower.panel(...) : 
  unused argument(s) (xlim = c(-1, 1), ylim = c(-1, 1))


  
[[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] pairs with same xlim and ylim scale

[Dejian Zhao]

I think you have successfully passed the xlim and ylim into the 
function pairs1. Compare the two graphs produced by the codes you 
provided, you can find the xlim and ylim in the second graph have been 
reset to the assigned value. It seems that the program halted in 
producing the second plot after adding xlim and ylim. According to the 
error message, the two added parameters were not used in lower.panel, or 
the customized function f.xy.


On 2010-9-1 2:26, Shi, Tao wrote:

Hi list,

I have a function which basically is a wrapper of pairs with some useful panel
functions.  However, I'm having trouble to pass the xlim and ylim into the
function so the x and y axes are in the same scale and 45 degree lines are
exactly diagonal.   I've looked at some old posts, they didn't help much.  I
think this is b/c I have multiple panel functions.  Help!

Thanks!

...Tao


pairs1- function(x, ...) {
 f.xy- function(x, y, ...) {
 points(x, y, ...)
 abline(0, 1, col = 2)
 }

 panel.cor- function(x, y, digits=2, prefix=, cex.cor) {
  usr- par(usr); on.exit(par(usr))
  par(usr = c(0, 1, 0, 1))
  r- abs(cor(x, y, method=p, use=pairwise.complete.obs))
  txt- format(c(r, 0.123456789), digits=digits)[1]
  txt- paste(prefix, txt, sep=)
  if(missing(cex.cor)) cex- 0.8/strwidth(txt)
  text(0.5, 0.5, txt, cex = cex * r)
  }

  panel.hist- function(x, ...) {
  usr- par(usr); on.exit(par(usr))
  par(usr = c(usr[1:2], 0, 1.5) )
  h- hist(x, plot = FALSE)
  breaks- h$breaks; nB- length(breaks)
  y- h$counts; y- y/max(y)
  rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
  }

 pairs(x, lower.panel=f.xy, upper.panel=panel.cor, diag.panel=panel.hist,
...)
}

   

x- rnorm(100, sd=0.2)
x- cbind(x=x-0.1, y=x+0.1)
pairs1(x)
pairs1(x, xlim=c(-1,1), ylim=c(-1,1))
 

Error in lower.panel(...) :
   unused argument(s) (xlim = c(-1, 1), ylim = c(-1, 1))



[[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.



__
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] pairs

[David Winsemius]

I'm not convinced it's right. In fact, I'm pretty sure the last step  
taking only the first half of the list is wrong. I also do not know if  
you have considered how you want to count situations like:


3 2 7 4 5 7 ...
7 3 8 6 1 2 9 2 ..

How many pairs of 2-7/7-2 would that represent?

--
David
On Nov 15, 2009, at 11:06 PM, cindy Guo wrote:


Hi, David,

The matrix has 20 columns.
Thank you very much for your help. I think it's right, but it seems  
I need some time to figure it out. I am a green hand. There are so  
many functions here I never used before. :)


Cindy

On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net 
 wrote:

Assuming that the number of columns is 4, then consider this approach:

 prs -scan()
1: 2 5 1 6
5: 1 7 8 2
9: 3 7 6 2
13: 9 8 5 7
17:
Read 16 items
prmtx - matrix(prs, 4,4, byrow=T)

#Now make copus of x.y and y.x

pair.str - sapply(1:nrow(prmtx), function(z)  
c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2],  
sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x)  
paste(x[2],x[1], sep=.))) )

tpair -table(pair.str)

# This then gives you a duplicated list
 tpair[tpair1]
pair.str
1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
 2   2   2   2   2   2   2   2

# So only take the first half of the pairs:
 head(tpair[tpair1], sum(tpair1)/2)

pair.str
1.2 2.1 2.6 2.7
 2   2   2   2

--
David.



On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

I could of course be wrong but have you yet specified the number of  
columns for this pairing exercise?


On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

Hi, All,

I have an n by m matrix with each entry between 1 and 15000. I want  
to know
the frequency of each pair in 1:15000 that occur together in rows.  
So for

example, if the matrix is
2 5 1 6
1 7 8 2
3 7 6 2
9 8 5 7
Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to  
return
the value 2 for this pair as well as that for all pairs. Is there a  
fast way

to do this avoiding loops? Loops take too long.

and provide commented, minimal, self-contained, reproducible code.
 ^^

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT




David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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] pairs

[David Winsemius]

I stuck in another 7 in one of the lines with a 2 and reasoned that  
we could deal with the desire for non-ordered pair counting by  
pasting min(x,y) to max(x,y);


 dput(prmtx)
structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim =  
c(4L,

4L))
 prmtx
 [,1] [,2] [,3] [,4]
[1,]2516
[2,]1772
[3,]3762
[4,]9857

 pair.str - sapply(1:nrow(prmtx), function(z)   
apply(combn(prmtx[z,], 2), 2,function(x) paste(min(x[2],x[1]),  
max(x[2],x[1]), sep=.)))


The logic:
sapply(1:nrow(prmtx), ... just loops over the rows of the matrix.
combn(prmtx[z,], 2)  ... returns a two row matrix of combination in a  
single row.
apply(combn(prmtx[z,], 2), 2 ... since combn( , 2)  returns a matrix  
that has two _rows_ I needed to loop over the columns.
paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the minimum  
of a pair in front of the max and separates them with a period to  
prevent two+ digits from being non-unique


Then using table() and logical tests in an index for the desired  
multiple pairs:



 tpair -table(pair.str)
 tpair
pair.str
1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8  
7.9 8.9
  2   1   1   2   1   1   2   3   1   1   1   1   1   1   1   1   1
1   1

 tpair[tpair1]
pair.str
1.2 1.7 2.6 2.7
  2   2   2   3

--
David.

On Nov 16, 2009, at 7:02 AM, David Winsemius wrote:

I'm not convinced it's right. In fact, I'm pretty sure the last step  
taking only the first half of the list is wrong. I also do not know  
if you have considered how you want to count situations like:


3 2 7 4 5 7 ...
7 3 8 6 1 2 9 2 ..

How many pairs of 2-7/7-2 would that represent?

--
David
On Nov 15, 2009, at 11:06 PM, cindy Guo wrote:


Hi, David,

The matrix has 20 columns.
Thank you very much for your help. I think it's right, but it seems  
I need some time to figure it out. I am a green hand. There are so  
many functions here I never used before. :)


Cindy

On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net 
 wrote:
Assuming that the number of columns is 4, then consider this  
approach:


 prs -scan()
1: 2 5 1 6
5: 1 7 8 2
9: 3 7 6 2
13: 9 8 5 7
17:
Read 16 items
prmtx - matrix(prs, 4,4, byrow=T)

#Now make copus of x.y and y.x

pair.str - sapply(1:nrow(prmtx), function(z)  
c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2],  
sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x)  
paste(x[2],x[1], sep=.))) )

tpair -table(pair.str)

# This then gives you a duplicated list
 tpair[tpair1]
pair.str
1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
2   2   2   2   2   2   2   2

# So only take the first half of the pairs:
 head(tpair[tpair1], sum(tpair1)/2)

pair.str
1.2 2.1 2.6 2.7
2   2   2   2

--
David.



On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

I could of course be wrong but have you yet specified the number of  
columns for this pairing exercise?


On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

Hi, All,

I have an n by m matrix with each entry between 1 and 15000. I want  
to know
the frequency of each pair in 1:15000 that occur together in rows.  
So for

example, if the matrix is
2 5 1 6
1 7 8 2
3 7 6 2
9 8 5 7
Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to  
return
the value 2 for this pair as well as that for all pairs. Is there a  
fast way

to do this avoiding loops? Loops take too long.

and provide commented, minimal, self-contained, reproducible code.
^^

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT




David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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] pairs

[cindy Guo]

I forgot to say that there are no ties in each row. So any number can occur
only once in each row. Also as I mentioned earlier, actually I only need the
top 50 most frequent pairs, is there a more efficient way to do it? Because
I have 15000 numbers, output of all the pairs would be too long.

Thank you,

Cindy

On Mon, Nov 16, 2009 at 7:02 AM, David Winsemius dwinsem...@comcast.netwrote:

 I stuck in another 7 in one of the lines with a 2 and reasoned that we
 could deal with the desire for non-ordered pair counting by pasting
 min(x,y) to max(x,y);

  dput(prmtx)
 structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim = c(4L,
 4L))
  prmtx
 [,1] [,2] [,3] [,4]
 [1,]2516
 [2,]1772
 [3,]3762
 [4,]9857

  pair.str - sapply(1:nrow(prmtx), function(z)  apply(combn(prmtx[z,], 2),
 2,function(x) paste(min(x[2],x[1]), max(x[2],x[1]), sep=.)))

 The logic:
 sapply(1:nrow(prmtx), ... just loops over the rows of the matrix.
 combn(prmtx[z,], 2)  ... returns a two row matrix of combination in a
 single row.
 apply(combn(prmtx[z,], 2), 2 ... since combn( , 2)  returns a matrix that
 has two _rows_ I needed to loop over the columns.
 paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the minimum of a
 pair in front of the max and separates them with a period to prevent two+
 digits from being non-unique

 Then using table() and logical tests in an index for the desired multiple
 pairs:


  tpair -table(pair.str)
  tpair
 pair.str
 1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8 7.9 8.9
  2   1   1   2   1   1   2   3   1   1   1   1   1   1   1   1   1   1   1

  tpair[tpair1]
 pair.str
 1.2 1.7 2.6 2.7
  2   2   2   3

 --
 David.


 On Nov 16, 2009, at 7:02 AM, David Winsemius wrote:

 I'm not convinced it's right. In fact, I'm pretty sure the last step taking
 only the first half of the list is wrong. I also do not know if you have
 considered how you want to count situations like:

 3 2 7 4 5 7 ...
 7 3 8 6 1 2 9 2 ..

 How many pairs of 2-7/7-2 would that represent?

 --
 David
 On Nov 15, 2009, at 11:06 PM, cindy Guo wrote:

 Hi, David,

 The matrix has 20 columns.
 Thank you very much for your help. I think it's right, but it seems I
 need some time to figure it out. I am a green hand. There are so many
 functions here I never used before. :)

 Cindy

 On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net
 wrote:
 Assuming that the number of columns is 4, then consider this approach:

  prs -scan()
 1: 2 5 1 6
 5: 1 7 8 2
 9: 3 7 6 2
 13: 9 8 5 7
 17:
 Read 16 items
 prmtx - matrix(prs, 4,4, byrow=T)

 #Now make copus of x.y and y.x

 pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,],
 2), 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,], 2),
 2,function(x) paste(x[2],x[1], sep=.))) )
 tpair -table(pair.str)

 # This then gives you a duplicated list
  tpair[tpair1]
 pair.str
 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
 2   2   2   2   2   2   2   2

 # So only take the first half of the pairs:
  head(tpair[tpair1], sum(tpair1)/2)

 pair.str
 1.2 2.1 2.6 2.7
 2   2   2   2

 --
 David.



 On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

 I could of course be wrong but have you yet specified the number of
 columns for this pairing exercise?

 On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

 Hi, All,

 I have an n by m matrix with each entry between 1 and 15000. I want to
 know
 the frequency of each pair in 1:15000 that occur together in rows. So for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
 the value 2 for this pair as well as that for all pairs. Is there a fast
 way
 to do this avoiding loops? Loops take too long.

 and provide commented, minimal, self-contained, reproducible code.
^^

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list

Re: [R] pairs

[David Winsemius]

On Nov 16, 2009, at 2:32 PM, cindy Guo wrote:

 I forgot to say that there are no ties in each row. So any number  
 can occur only once in each row. Also as I mentioned earlier,  
 actually I only need the top 50 most frequent pairs, is there a more  
 efficient way to do it? Because I have 15000 numbers, output of all  
 the pairs would be too long.

?order



 Thank you,

 Cindy

 On Mon, Nov 16, 2009 at 7:02 AM, David Winsemius dwinsem...@comcast.net 
  wrote:
 I stuck in another 7 in one of the lines with a 2 and reasoned  
 that we could deal with the desire for non-ordered pair counting  
 by pasting min(x,y) to max(x,y);

  dput(prmtx)
 structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim =  
 c(4L,
 4L))
  prmtx
 [,1] [,2] [,3] [,4]
 [1,]2516
 [2,]1772
 [3,]3762
 [4,]9857

  pair.str - sapply(1:nrow(prmtx), function(z)   
 apply(combn(prmtx[z,], 2), 2,function(x) paste(min(x[2],x[1]),  
 max(x[2],x[1]), sep=.)))

 The logic:
 sapply(1:nrow(prmtx), ... just loops over the rows of the matrix.
 combn(prmtx[z,], 2)  ... returns a two row matrix of combination in  
 a single row.
 apply(combn(prmtx[z,], 2), 2 ... since combn( , 2)  returns a matrix  
 that has two _rows_ I needed to loop over the columns.
 paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the minimum  
 of a pair in front of the max and separates them with a period to  
 prevent two+ digits from being non-unique

 Then using table() and logical tests in an index for the desired  
 multiple pairs:


  tpair -table(pair.str)
  tpair
 pair.str
 1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8  
 7.9 8.9
  2   1   1   2   1   1   2   3   1   1   1   1   1   1   1   1   1
 1   1

  tpair[tpair1]
 pair.str
 1.2 1.7 2.6 2.7
  2   2   2   3

 -- 
 David.


 On Nov 16, 2009, at 7:02 AM, David Winsemius wrote:

 I'm not convinced it's right. In fact, I'm pretty sure the last step  
 taking only the first half of the list is wrong. I also do not know  
 if you have considered how you want to count situations like:

 3 2 7 4 5 7 ...
 7 3 8 6 1 2 9 2 ..

 How many pairs of 2-7/7-2 would that represent?

 -- 
 David
 On Nov 15, 2009, at 11:06 PM, cindy Guo wrote:

 Hi, David,

 The matrix has 20 columns.
 Thank you very much for your help. I think it's right, but it seems  
 I need some time to figure it out. I am a green hand. There are so  
 many functions here I never used before. :)

 Cindy

 On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net 
  wrote:
 Assuming that the number of columns is 4, then consider this approach:

  prs -scan()
 1: 2 5 1 6
 5: 1 7 8 2
 9: 3 7 6 2
 13: 9 8 5 7
 17:
 Read 16 items
 prmtx - matrix(prs, 4,4, byrow=T)

 #Now make copus of x.y and y.x

 pair.str - sapply(1:nrow(prmtx), function(z)  
 c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2],  
 sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x)  
 paste(x[2],x[1], sep=.))) )
 tpair -table(pair.str)

 # This then gives you a duplicated list
  tpair[tpair1]
 pair.str
 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
 2   2   2   2   2   2   2   2

 # So only take the first half of the pairs:
  head(tpair[tpair1], sum(tpair1)/2)

 pair.str
 1.2 2.1 2.6 2.7
 2   2   2   2

 -- 
 David.



 On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

 I could of course be wrong but have you yet specified the number of  
 columns for this pairing exercise?

 On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

 Hi, All,

 I have an n by m matrix with each entry between 1 and 15000. I want  
 to know
 the frequency of each pair in 1:15000 that occur together in rows.  
 So for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to  
 return
 the value 2 for this pair as well as that for all pairs. Is there a  
 fast way
 to do this avoiding loops? Loops take too long.

 and provide commented, minimal, self-contained, reproducible code.
^^

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



David Winsemius, MD
Heritage Laboratories
West Hartford, CT


[[alternative HTML 

Re: [R] pairs

[cindy Guo]

Do you mean if the numbers in each row are ordered? They are not, but if
it's needed, we can order them. The matrix only has 5000 rows.

On Mon, Nov 16, 2009 at 1:34 PM, David Winsemius dwinsem...@comcast.netwrote:


  On Nov 16, 2009, at 2:32 PM, cindy Guo wrote:

  I forgot to say that there are no ties in each row. So any number can
 occur only once in each row. Also as I mentioned earlier, actually I only
 need the top 50 most frequent pairs, is there a more efficient way to do it?
 Because I have 15000 numbers, output of all the pairs would be too long.


 ?order



 Thank you,

 Cindy

 On Mon, Nov 16, 2009 at 7:02 AM, David Winsemius 
 dwinsem...@comcast.netwrote:

 I stuck in another 7 in one of the lines with a 2 and reasoned that we
 could deal with the desire for non-ordered pair counting by pasting
 min(x,y) to max(x,y);

  dput(prmtx)
 structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim = c(4L,
 4L))
  prmtx
 [,1] [,2] [,3] [,4]
 [1,]2516
 [2,]1772
 [3,]3762
 [4,]9857

  pair.str - sapply(1:nrow(prmtx), function(z)  apply(combn(prmtx[z,],
 2), 2,function(x) paste(min(x[2],x[1]), max(x[2],x[1]), sep=.)))

 The logic:
 sapply(1:nrow(prmtx), ... just loops over the rows of the matrix.
 combn(prmtx[z,], 2)  ... returns a two row matrix of combination in a
 single row.
 apply(combn(prmtx[z,], 2), 2 ... since combn( , 2)  returns a matrix that
 has two _rows_ I needed to loop over the columns.
 paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the minimum of a
 pair in front of the max and separates them with a period to prevent two+
 digits from being non-unique

 Then using table() and logical tests in an index for the desired multiple
 pairs:


  tpair -table(pair.str)
  tpair
 pair.str
 1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8 7.9
 8.9
  2   1   1   2   1   1   2   3   1   1   1   1   1   1   1   1   1   1   1


  tpair[tpair1]
 pair.str
 1.2 1.7 2.6 2.7
  2   2   2   3

 --
 David.


 On Nov 16, 2009, at 7:02 AM, David Winsemius wrote:

 I'm not convinced it's right. In fact, I'm pretty sure the last step
 taking only the first half of the list is wrong. I also do not know if you
 have considered how you want to count situations like:

 3 2 7 4 5 7 ...
 7 3 8 6 1 2 9 2 ..

 How many pairs of 2-7/7-2 would that represent?

 --
 David
 On Nov 15, 2009, at 11:06 PM, cindy Guo wrote:

 Hi, David,

 The matrix has 20 columns.
 Thank you very much for your help. I think it's right, but it seems I
 need some time to figure it out. I am a green hand. There are so many
 functions here I never used before. :)

 Cindy

 On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius 
 dwinsem...@comcast.net wrote:
 Assuming that the number of columns is 4, then consider this approach:

  prs -scan()
 1: 2 5 1 6
 5: 1 7 8 2
 9: 3 7 6 2
 13: 9 8 5 7
 17:
 Read 16 items
 prmtx - matrix(prs, 4,4, byrow=T)

 #Now make copus of x.y and y.x

 pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,],
 2), 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,], 2),
 2,function(x) paste(x[2],x[1], sep=.))) )
 tpair -table(pair.str)

 # This then gives you a duplicated list
  tpair[tpair1]
 pair.str
 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
 2   2   2   2   2   2   2   2

 # So only take the first half of the pairs:
  head(tpair[tpair1], sum(tpair1)/2)

 pair.str
 1.2 2.1 2.6 2.7
 2   2   2   2

 --
 David.



 On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

 I could of course be wrong but have you yet specified the number of
 columns for this pairing exercise?

 On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

 Hi, All,

 I have an n by m matrix with each entry between 1 and 15000. I want to
 know
 the frequency of each pair in 1:15000 that occur together in rows. So
 for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to
 return
 the value 2 for this pair as well as that for all pairs. Is there a fast
 way
 to do this avoiding loops? Loops take too long.

 and provide commented, minimal, self-contained, reproducible code.
^^

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 

Re: [R] pairs

[cls59]

David Winsemius wrote:
 
 ?order
 

cindy Guo wrote:
 
 Do you mean if the numbers in each row are ordered? They are not, but if
 it's needed, we can order them. The matrix only has 5000 rows.
 

No, he's suggesting you check out the order() function by calling it's help
page:

  ?order

order() will sort your results into ascending or descending order.  You
could then pick off the top 50 by using head().

Hope that helps!

-Charlie


-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
-- 
View this message in context: 
http://old.nabble.com/pairs-tp26364801p26378236.html
Sent from the R help mailing list archive at Nabble.com.

__
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] pairs

[David Winsemius]

On Nov 16, 2009, at 2:41 PM, cindy Guo wrote:

 Do you mean if the numbers in each row are ordered? They are not,  
 but if it's needed, we can order them. The matrix only has 5000 rows.


No, I mean type ?order at the R command line and read the help page.

 On Mon, Nov 16, 2009 at 1:34 PM, David Winsemius dwinsem...@comcast.net 
  wrote:

 On Nov 16, 2009, at 2:32 PM, cindy Guo wrote:

 I forgot to say that there are no ties in each row. So any number  
 can occur only once in each row. Also as I mentioned earlier,  
 actually I only need the top 50 most frequent pairs, is there a  
 more efficient way to do it? Because I have 15000 numbers, output  
 of all the pairs would be too long.

 ?order



 Thank you,

 Cindy

 On Mon, Nov 16, 2009 at 7:02 AM, David Winsemius dwinsem...@comcast.net 
  wrote:
 I stuck in another 7 in one of the lines with a 2 and reasoned  
 that we could deal with the desire for non-ordered pair counting  
 by pasting min(x,y) to max(x,y);

  dput(prmtx)
 structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim =  
 c(4L,
 4L))
  prmtx
 [,1] [,2] [,3] [,4]
 [1,]2516
 [2,]1772
 [3,]3762
 [4,]9857

  pair.str - sapply(1:nrow(prmtx), function(z)   
 apply(combn(prmtx[z,], 2), 2,function(x) paste(min(x[2],x[1]),  
 max(x[2],x[1]), sep=.)))

 The logic:
 sapply(1:nrow(prmtx), ... just loops over the rows of the matrix.
 combn(prmtx[z,], 2)  ... returns a two row matrix of combination in  
 a single row.
 apply(combn(prmtx[z,], 2), 2 ... since combn( , 2)  returns a  
 matrix that has two _rows_ I needed to loop over the columns.
 paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the  
 minimum of a pair in front of the max and separates them with a  
 period to prevent two+ digits from being non-unique

 Then using table() and logical tests in an index for the desired  
 multiple pairs:


  tpair -table(pair.str)
  tpair
 pair.str
 1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8  
 7.9 8.9
  2   1   1   2   1   1   2   3   1   1   1   1   1   1   1   1
 1   1   1

  tpair[tpair1]
 pair.str
 1.2 1.7 2.6 2.7
  2   2   2   3

 -- 
 David.


 On Nov 16, 2009, at 7:02 AM, David Winsemius wrote:

 I'm not convinced it's right. In fact, I'm pretty sure the last  
 step taking only the first half of the list is wrong. I also do not  
 know if you have considered how you want to count situations like:

 3 2 7 4 5 7 ...
 7 3 8 6 1 2 9 2 ..

 How many pairs of 2-7/7-2 would that represent?

 -- 
 David
 On Nov 15, 2009, at 11:06 PM, cindy Guo wrote:

 Hi, David,

 The matrix has 20 columns.
 Thank you very much for your help. I think it's right, but it seems  
 I need some time to figure it out. I am a green hand. There are so  
 many functions here I never used before. :)

 Cindy

 On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net 
  wrote:
 Assuming that the number of columns is 4, then consider this  
 approach:

  prs -scan()
 1: 2 5 1 6
 5: 1 7 8 2
 9: 3 7 6 2
 13: 9 8 5 7
 17:
 Read 16 items
 prmtx - matrix(prs, 4,4, byrow=T)

 #Now make copus of x.y and y.x

 pair.str - sapply(1:nrow(prmtx), function(z)  
 c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2],  
 sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x)  
 paste(x[2],x[1], sep=.))) )
 tpair -table(pair.str)

 # This then gives you a duplicated list
  tpair[tpair1]
 pair.str
 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
 2   2   2   2   2   2   2   2

 # So only take the first half of the pairs:
  head(tpair[tpair1], sum(tpair1)/2)

 pair.str
 1.2 2.1 2.6 2.7
 2   2   2   2

 -- 
 David.



 On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

 I could of course be wrong but have you yet specified the number of  
 columns for this pairing exercise?

 On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

 Hi, All,

 I have an n by m matrix with each entry between 1 and 15000. I want  
 to know
 the frequency of each pair in 1:15000 that occur together in rows.  
 So for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to  
 return
 the value 2 for this pair as well as that for all pairs. Is there a  
 fast way
 to do this avoiding loops? Loops take too long.

 and provide commented, minimal, self-contained, reproducible code.
^^

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 R-help@r-project.org mailing list
 

Re: [R] pairs

[cindy Guo]

Thank you. I will check that.
Cindy

On Mon, Nov 16, 2009 at 1:45 PM, cls59 ch...@sharpsteen.net wrote:



 David Winsemius wrote:
 
  ?order
 

 cindy Guo wrote:
 
  Do you mean if the numbers in each row are ordered? They are not, but if
  it's needed, we can order them. The matrix only has 5000 rows.
 

 No, he's suggesting you check out the order() function by calling it's help
 page:

  ?order

 order() will sort your results into ascending or descending order.  You
 could then pick off the top 50 by using head().

 Hope that helps!

 -Charlie


 -
 Charlie Sharpsteen
 Undergraduate
 Environmental Resources Engineering
 Humboldt State University
 --
 View this message in context:
 http://old.nabble.com/pairs-tp26364801p26378236.html
 Sent from the R help mailing list archive at Nabble.com.

 __
  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.htmlhttp://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.

[R] pairs

[cindy Guo]

Hi, All,

I have an n by m matrix with each entry between 1 and 15000. I want to know
the frequency of each pair in 1:15000 that occur together in rows. So for
example, if the matrix is
2 5 1 6
1 7 8 2
3 7 6 2
9 8 5 7
Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
the value 2 for this pair as well as that for all pairs. Is there a fast way
to do this avoiding loops? Loops take too long.

Thank you,

Cindy

[[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] pairs

[cls59]

cindy Guo wrote:
 
 Hi, All,
 
 I have an n by m matrix with each entry between 1 and 15000. I want to
 know
 the frequency of each pair in 1:15000 that occur together in rows. So for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
 the value 2 for this pair as well as that for all pairs. Is there a fast
 way
 to do this avoiding loops? Loops take too long.
 
 Thank you,
 
 Cindy
 

Use %in% to check for the presence of the numbers in a row and apply() to
efficiently execute the test for each row:

 tstMatrix - matrix( c(2,5,1,6,
1,7,8,2,
3,7,6,2,
9,8,5,7), nrow=4, byrow=T )

  matches - apply( tstMatrix, 1, function( row ){
   
if( 2 %in% row  6 %in% row ){

  return( 2 )

} else {

  return( 0 )

}

  })

  matches
  [1] 2 0 2 0

If you have more than one pair, it gets a little tricky.  Say you are also
looking for the pair (7,8).  Store them as a list:

  pairList - list( c(2,6), c(7,8) )

Then use sapply() to efficiently iterate over the pair list and execute the
apply() test:

  matchMatrix - sapply( pairList, function( pair ){

matches - apply( tstMatrix, 1, function( row ){

  if( pair[1] %in% row  pair[2] %in% row ){

return( pair[1] )

  } else {

return( 0 )

  }

})

return( matches )

  })

  matchMatrix

   [,1] [,2]
  [1,]20
  [2,]07
  [3,]20
  [4,]07



If you're looking to apply the above method to every possible permutation of
2 numbers that may be generated from the range of numbers 1:15000... that's
225,000,000 pairs. expand.grid() can generate the required pair list-- but
that step alone causes a memory allocation of ~6 GB on my machine.

If you don't have a pile of CPU cores and RAM at your disposal, you can
probably:

  1. Restrict the upper end of your range to the maximal entry present in
your matrix since all other combinations have zero occurrences.

  2. Break the list of pairs up into several sublists, run the tests, and
aggregate the results.

Either way, the analysis will take some time despite the efficiencies of the
apply family of functions due to the shear size of the problem.  If you have
more than one CPU, I would recommend taking a look at parallelized apply
functions, perhaps using a package like snowfall,  as the testing of the
pairs is an embarrassingly parallel problem.

Hopefully I'm misunderstanding the scope of your problem.


Good luck!

-Charlie

-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
-- 
View this message in context: 
http://old.nabble.com/pairs-tp26364801p26365206.html
Sent from the R help mailing list archive at Nabble.com.

__
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] pairs

[Linlin Yan]

Hope this help:

 m - matrix(c(2,1,3,9,5,7,7,8,1,8,6,5,6,2,2,7),4,4)
 p - c(2, 6)

 apply(m == p[1], 1, any)  apply(m == p[2], 1, any)
[1]  TRUE FALSE  TRUE FALSE

If you want the number of rows which contain the pair, sum() could be used:

 sum(apply(m == p[1], 1, any)  apply(m == p[2], 1, any))
[1] 2

On Mon, Nov 16, 2009 at 6:26 AM, cindy Guo cindy.g...@gmail.com wrote:
 Hi, All,

 I have an n by m matrix with each entry between 1 and 15000. I want to know
 the frequency of each pair in 1:15000 that occur together in rows. So for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
 the value 2 for this pair as well as that for all pairs. Is there a fast way
 to do this avoiding loops? Loops take too long.

 Thank you,

 Cindy

        [[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.


__
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] pairs

[cindy Guo]

Hi, Charlie,

Thank you for the reply. Maybe I don't need the frequency of each pair. I
only need the top, say 50, pairs with the highest frequency. Is there anyway
which can avoid calculating for all the pairs?

Thanks,

Cindy
On Sun, Nov 15, 2009 at 4:18 PM, cls59 ch...@sharpsteen.net wrote:




 cindy Guo wrote:
 
  Hi, All,
 
  I have an n by m matrix with each entry between 1 and 15000. I want to
  know
  the frequency of each pair in 1:15000 that occur together in rows. So for
  example, if the matrix is
  2 5 1 6
  1 7 8 2
  3 7 6 2
  9 8 5 7
  Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
  the value 2 for this pair as well as that for all pairs. Is there a fast
  way
  to do this avoiding loops? Loops take too long.
 
  Thank you,
 
  Cindy
 

 Use %in% to check for the presence of the numbers in a row and apply() to
 efficiently execute the test for each row:

  tstMatrix - matrix( c(2,5,1,6,
1,7,8,2,
3,7,6,2,
9,8,5,7), nrow=4, byrow=T )

  matches - apply( tstMatrix, 1, function( row ){

if( 2 %in% row  6 %in% row ){

  return( 2 )

} else {

  return( 0 )

}

  })

  matches
  [1] 2 0 2 0

 If you have more than one pair, it gets a little tricky.  Say you are also
 looking for the pair (7,8).  Store them as a list:

  pairList - list( c(2,6), c(7,8) )

 Then use sapply() to efficiently iterate over the pair list and execute the
 apply() test:

  matchMatrix - sapply( pairList, function( pair ){

matches - apply( tstMatrix, 1, function( row ){

  if( pair[1] %in% row  pair[2] %in% row ){

return( pair[1] )

  } else {

return( 0 )

  }

})

return( matches )

  })

  matchMatrix

   [,1] [,2]
  [1,]20
  [2,]07
  [3,]20
  [4,]07



 If you're looking to apply the above method to every possible permutation
 of
 2 numbers that may be generated from the range of numbers 1:15000... that's
 225,000,000 pairs. expand.grid() can generate the required pair list-- but
 that step alone causes a memory allocation of ~6 GB on my machine.

 If you don't have a pile of CPU cores and RAM at your disposal, you can
 probably:

  1. Restrict the upper end of your range to the maximal entry present in
 your matrix since all other combinations have zero occurrences.

  2. Break the list of pairs up into several sublists, run the tests, and
 aggregate the results.

 Either way, the analysis will take some time despite the efficiencies of
 the
 apply family of functions due to the shear size of the problem.  If you
 have
 more than one CPU, I would recommend taking a look at parallelized apply
 functions, perhaps using a package like snowfall,  as the testing of the
 pairs is an embarrassingly parallel problem.

 Hopefully I'm misunderstanding the scope of your problem.


 Good luck!

 -Charlie

 -
 Charlie Sharpsteen
 Undergraduate
 Environmental Resources Engineering
 Humboldt State University
 --
 View this message in context:
 http://old.nabble.com/pairs-tp26364801p26365206.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 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.htmlhttp://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.

Re: [R] pairs

[David Winsemius]

I could of course be wrong but have you yet specified the number of  
columns for this pairing exercise?


On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:


Hi, All,

I have an n by m matrix with each entry between 1 and 15000. I want  
to know
the frequency of each pair in 1:15000 that occur together in rows.  
So for

example, if the matrix is
2 5 1 6
1 7 8 2
3 7 6 2
9 8 5 7
Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to  
return
the value 2 for this pair as well as that for all pairs. Is there a  
fast way

to do this avoiding loops? Loops take too long.

and provide commented, minimal, self-contained, reproducible code.

   ^^

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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] pairs

[David Winsemius]

Assuming that the number of columns is 4, then consider this approach:

 prs -scan()
1: 2 5 1 6
5: 1 7 8 2
9: 3 7 6 2
13: 9 8 5 7
17:
Read 16 items
prmtx - matrix(prs, 4,4, byrow=T)

#Now make copus of x.y and y.x

pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,],  
2), 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,],  
2), 2,function(x) paste(x[2],x[1], sep=.))) )

tpair -table(pair.str)

# This then gives you a duplicated list
 tpair[tpair1]
pair.str
1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
  2   2   2   2   2   2   2   2

# So only take the first half of the pairs:
 head(tpair[tpair1], sum(tpair1)/2)

pair.str
1.2 2.1 2.6 2.7
  2   2   2   2

--
David.


On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

I could of course be wrong but have you yet specified the number of  
columns for this pairing exercise?


On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:


Hi, All,

I have an n by m matrix with each entry between 1 and 15000. I want  
to know
the frequency of each pair in 1:15000 that occur together in rows.  
So for

example, if the matrix is
2 5 1 6
1 7 8 2
3 7 6 2
9 8 5 7
Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to  
return
the value 2 for this pair as well as that for all pairs. Is there a  
fast way

to do this avoiding loops? Loops take too long.

and provide commented, minimal, self-contained, reproducible code.

  ^^

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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] pairs

[cindy Guo]

Hi, David,

The matrix has 20 columns.
Thank you very much for your help. I think it's right, but it seems I need
some time to figure it out. I am a green hand. There are so many functions
here I never used before. :)

Cindy

On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.netwrote:

 Assuming that the number of columns is 4, then consider this approach:

  prs -scan()
 1: 2 5 1 6
 5: 1 7 8 2
 9: 3 7 6 2
 13: 9 8 5 7
 17:
 Read 16 items
 prmtx - matrix(prs, 4,4, byrow=T)

 #Now make copus of x.y and y.x

 pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,], 2),
 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,], 2),
 2,function(x) paste(x[2],x[1], sep=.))) )
 tpair -table(pair.str)

 # This then gives you a duplicated list
  tpair[tpair1]
 pair.str
 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7
  2   2   2   2   2   2   2   2

 # So only take the first half of the pairs:
  head(tpair[tpair1], sum(tpair1)/2)

 pair.str
 1.2 2.1 2.6 2.7
  2   2   2   2

 --
 David.



 On Nov 15, 2009, at 8:06 PM, David Winsemius wrote:

   I could of course be wrong but have you yet specified the number of
 columns for this pairing exercise?

 On Nov 15, 2009, at 5:26 PM, cindy Guo wrote:

 Hi, All,

 I have an n by m matrix with each entry between 1 and 15000. I want to
 know
 the frequency of each pair in 1:15000 that occur together in rows. So for
 example, if the matrix is
 2 5 1 6
 1 7 8 2
 3 7 6 2
 9 8 5 7
 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
 the value 2 for this pair as well as that for all pairs. Is there a fast
 way
 to do this avoiding loops? Loops take too long.

 and provide commented, minimal, self-contained, reproducible code.

  ^^

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 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.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



[[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.

[R] pairs

[Seyit Ali Kayis]

Dear all, 

 

I have two sets of data (say set1 and set2) as follow:

 

set1







x1
x2
x3

0.30
0.43
3.88

0.38
0.59
3.53

0.30
0.42
2.12

0.33
0.53
2.12

0.30
0.47
3.76

 

set2







y1
y2
y3

0.32
0.47
5.18

0.23
0.26
1.06

0.42
0.65
3.88

0.28
0.38
3.76

0.35
0.47
1.41

 

The pairs function (such as pairs(~x1+x2+x3 data=set1, main=Simple 
Scatterplot Matrix) ) is producing scatterplot matrix where lower and upper 
diagonals have scatter plots of set1 variables. 

 

I want to produce a scatterplot matrix where in upper panel (diagonal) I should 
have plots from set1 variables and in lower panel (diagonal) I should have 
plots from set2 variables. Is there a way that I can do this?

 

Any help is deeply appreciated.

 

Kind Regards

 

Seyit Ali



--
 
Dr. Seyit Ali KAYIS
Selcuk University
Faculty of Agriculture
Kampus, Konya, TURKEY

s_a_ka...@yahoo.com,s_a_ka...@hotmail.com
Tell: +90 332 223 2830  Mobile: +90 535 587 1139  Fax: +90 332 241 0108

   Greetings from Konya, TURKEY
http://www.ziraat.selcuk.edu.tr/skayis/
--
 






  
_

 Facebook.

k-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-nz:SI_SB_2:092010
[[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] pairs

[Greg Snow]

Does the pairs2 function in the TeachingDemos package do what you want?

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Seyit Ali Kayis
 Sent: Wednesday, October 14, 2009 6:35 AM
 To: r-help@r-project.org
 Subject: [R] pairs
 
 
 Dear all,
 
 
 
 I have two sets of data (say set1 and set2) as follow:
 
 
 
 set1
 
 
 
 
 
 
 
 x1
 x2
 x3
 
 0.30
 0.43
 3.88
 
 0.38
 0.59
 3.53
 
 0.30
 0.42
 2.12
 
 0.33
 0.53
 2.12
 
 0.30
 0.47
 3.76
 
 
 
 set2
 
 
 
 
 
 
 
 y1
 y2
 y3
 
 0.32
 0.47
 5.18
 
 0.23
 0.26
 1.06
 
 0.42
 0.65
 3.88
 
 0.28
 0.38
 3.76
 
 0.35
 0.47
 1.41
 
 
 
 The pairs function (such as pairs(~x1+x2+x3 data=set1, main=Simple
 Scatterplot Matrix) ) is producing scatterplot matrix where lower and
 upper diagonals have scatter plots of set1 variables.
 
 
 
 I want to produce a scatterplot matrix where in upper panel (diagonal)
 I should have plots from set1 variables and in lower panel (diagonal) I
 should have plots from set2 variables. Is there a way that I can do
 this?
 
 
 
 Any help is deeply appreciated.
 
 
 
 Kind Regards
 
 
 
 Seyit Ali
 
 
 
 ---
 ---
 Dr. Seyit Ali KAYIS
 Selcuk University
 Faculty of Agriculture
 Kampus, Konya, TURKEY
 
 s_a_ka...@yahoo.com,s_a_ka...@hotmail.com
 Tell: +90 332 223 2830  Mobile: +90 535 587 1139  Fax: +90 332 241 0108
 
Greetings from Konya, TURKEY
 http://www.ziraat.selcuk.edu.tr/skayis/
 ---
 ---
 
 
 
 
 
 
 
 _
 
  Facebook.
 
 k-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-nz:SI_SB_2:092010
   [[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.

__
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] pairs

[Greg Snow]

Looking at the question again, I don't think pairs2 is the answer.  I think it 
will be easier to do this by hand than to get pairs to do it for you (though 
you could make your own function as a modification of pairs).

Does this do what you want?

xx - matrix(scan(), ncol=3, byrow=TRUE)
0.30
0.43
3.88
0.38
0.59
3.53
0.30
0.42
2.12
0.33
0.53
2.12
0.30
0.47
3.76

yy - matrix(scan(), ncol=3, byrow=TRUE)
0.32
0.47
5.18
0.23
0.26
1.06
0.42
0.65
3.88
0.28
0.38
3.76
0.35
0.47
1.41


par(mfrow=c(3,3), oma=c(4,4,4,4)+0.1, mar=c(0,0,0,0)+0.1)
for(i in 1:3) {
  for( j in 1:3 ) {
if(i==j) plot(1,1, pch=as.character(i), ann=FALSE, axes=FALSE, cex=5)
if(i  j ) plot( xx[,j], xx[,i], ann=FALSE, axes=FALSE  )
if(i  j ) plot( yy[,j], yy[,i], ann=FALSE, axes=FALSE )
box()
if( i  j ){ axis(4, outer=TRUE); axis(3, outer=TRUE) }
if( i  j ){ axis(1, outer=TRUE); axis(2, outer=TRUE) }
  }
}


-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Greg Snow
 Sent: Wednesday, October 14, 2009 11:13 AM
 To: Seyit Ali Kayis; r-help@r-project.org
 Subject: Re: [R] pairs
 
 Does the pairs2 function in the TeachingDemos package do what you want?
 
 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data Center
 Intermountain Healthcare
 greg.s...@imail.org
 801.408.8111
 
 
  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
  project.org] On Behalf Of Seyit Ali Kayis
  Sent: Wednesday, October 14, 2009 6:35 AM
  To: r-help@r-project.org
  Subject: [R] pairs
 
 
  Dear all,
 
 
 
  I have two sets of data (say set1 and set2) as follow:
 
 
 
  set1
 
 
 
 
 
 
 
  x1
  x2
  x3
 
  0.30
  0.43
  3.88
 
  0.38
  0.59
  3.53
 
  0.30
  0.42
  2.12
 
  0.33
  0.53
  2.12
 
  0.30
  0.47
  3.76
 
 
 
  set2
 
 
 
 
 
 
 
  y1
  y2
  y3
 
  0.32
  0.47
  5.18
 
  0.23
  0.26
  1.06
 
  0.42
  0.65
  3.88
 
  0.28
  0.38
  3.76
 
  0.35
  0.47
  1.41
 
 
 
  The pairs function (such as pairs(~x1+x2+x3 data=set1, main=Simple
  Scatterplot Matrix) ) is producing scatterplot matrix where lower
 and
  upper diagonals have scatter plots of set1 variables.
 
 
 
  I want to produce a scatterplot matrix where in upper panel
 (diagonal)
  I should have plots from set1 variables and in lower panel (diagonal)
 I
  should have plots from set2 variables. Is there a way that I can do
  this?
 
 
 
  Any help is deeply appreciated.
 
 
 
  Kind Regards
 
 
 
  Seyit Ali
 
 
 
  -
 --
  ---
  Dr. Seyit Ali KAYIS
  Selcuk University
  Faculty of Agriculture
  Kampus, Konya, TURKEY
 
  s_a_ka...@yahoo.com,s_a_ka...@hotmail.com
  Tell: +90 332 223 2830  Mobile: +90 535 587 1139  Fax: +90 332 241
 0108
 
 Greetings from Konya, TURKEY
  http://www.ziraat.selcuk.edu.tr/skayis/
  -
 --
  ---
 
 
 
 
 
 
 
  _
 
   Facebook.
 
  k-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-nz:SI_SB_2:092010
  [[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.
 
 __
 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-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] pairs plot

[Jose Narillos de Santos]

Hi Greg I saw, read, the TeachingDemos you suggesttef but when run pairs2
function on my R module says Can´t find function pairs2

How can I load the module or function pairs2?

Thanks in advance for your help.

You are the best.

2009/7/27, Greg Snow greg.s...@imail.org:

 Look at the pairs2 function in the TeachingDemos package.

 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data Center
 Intermountain Healthcare
 greg.s...@imail.org
 801.408.8111


  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
  project.org] On Behalf Of Jose Narillos de Santos
  Sent: Monday, July 27, 2009 9:02 AM
  To: r-help@r-project.org
  Subject: [R] pairs plot
 
  Hi all,
 
  I want to plot trough pairs() plot a matrix with 4 columns. I want to
  make a
  trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X
  axis.
 
  You mean (a plot with three graphs) ommitting the first pair with
  itself.
  And only the pairs with colum 1 with the other not all pairs.
 
  I. e. this matrix
 
  4177 289390 8740 17220
  3907 301510 8530 17550
  3975 316970 8640 17650
  3651 364220 9360 21420
  3031 387390 9960 23410
  2912 430180 11040 25820
  3018 499930 12240 27620
  2685 595010 13800 31670
  2884 661870 14760 37170
 
  Thanks in advance.
 
[[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.

Re: [R] pairs plot

[Petr PIKAL]

Hi

r-help-boun...@r-project.org napsal dne 28.07.2009 09:55:11:

 Hi Greg I saw, read, the TeachingDemos you suggesttef but when run 
pairs2
 function on my R module says Can´t find function pairs2
 
 How can I load the module or function pairs2?

Did you do

library(TeachingDemos)?

Regards
Petr


 
 Thanks in advance for your help.
 
 You are the best.
 
 2009/7/27, Greg Snow greg.s...@imail.org:
 
  Look at the pairs2 function in the TeachingDemos package.
 
  --
  Gregory (Greg) L. Snow Ph.D.
  Statistical Data Center
  Intermountain Healthcare
  greg.s...@imail.org
  801.408.8111
 
 
   -Original Message-
   From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
   project.org] On Behalf Of Jose Narillos de Santos
   Sent: Monday, July 27, 2009 9:02 AM
   To: r-help@r-project.org
   Subject: [R] pairs plot
  
   Hi all,
  
   I want to plot trough pairs() plot a matrix with 4 columns. I want 
to
   make a
   trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on 
X
   axis.
  
   You mean (a plot with three graphs) ommitting the first pair with
   itself.
   And only the pairs with colum 1 with the other not all pairs.
  
   I. e. this matrix
  
   4177 289390 8740 17220
   3907 301510 8530 17550
   3975 316970 8640 17650
   3651 364220 9360 21420
   3031 387390 9960 23410
   2912 430180 11040 25820
   3018 499930 12240 27620
   2685 595010 13800 31670
   2884 661870 14760 37170
  
   Thanks in advance.
  
 [[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.

__
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] pairs plot

[Jose Narillos de Santos]

Hi,

I tried to load typing library(TeachingDemos)

But the message can´t find package TeachingDemos) occurs. I use versión
R 2.9 on windows.

Can you please guide me?

Sorry¡¡¡





2009/7/28, Petr PIKAL petr.pi...@precheza.cz:

 Hi

 r-help-boun...@r-project.org napsal dne 28.07.2009 09:55:11:

  Hi Greg I saw, read, the TeachingDemos you suggesttef but when run
 pairs2
  function on my R module says Can´t find function pairs2
 
  How can I load the module or function pairs2?

 Did you do

 library(TeachingDemos)?

 Regards
 Petr


 
  Thanks in advance for your help.
 
  You are the best.
 
  2009/7/27, Greg Snow greg.s...@imail.org:
  
   Look at the pairs2 function in the TeachingDemos package.
  
   --
   Gregory (Greg) L. Snow Ph.D.
   Statistical Data Center
   Intermountain Healthcare
   greg.s...@imail.org
   801.408.8111
  
  
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Jose Narillos de Santos
Sent: Monday, July 27, 2009 9:02 AM
To: r-help@r-project.org
Subject: [R] pairs plot
   
Hi all,
   
I want to plot trough pairs() plot a matrix with 4 columns. I want
 to
make a
trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on
 X
axis.
   
You mean (a plot with three graphs) ommitting the first pair with
itself.
And only the pairs with colum 1 with the other not all pairs.
   
I. e. this matrix
   
4177 289390 8740 17220
3907 301510 8530 17550
3975 316970 8640 17650
3651 364220 9360 21420
3031 387390 9960 23410
2912 430180 11040 25820
3018 499930 12240 27620
2685 595010 13800 31670
2884 661870 14760 37170
   
Thanks in advance.
   
  [[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.



[[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] pairs plot

[John Kane]

Have you installed it first?  
First: 
install.packages(TeachingDemos)
Then:
library(TeachingDemos)


--- On Tue, 7/28/09, Jose Narillos de Santos narillosdesan...@gmail.com wrote:

 From: Jose Narillos de Santos narillosdesan...@gmail.com
 Subject: Re: [R] pairs plot
 To: Petr PIKAL petr.pi...@precheza.cz, r-help@r-project.org, 
 greg.s...@imail.org
 Received: Tuesday, July 28, 2009, 8:24 AM
 Hi,
 
 I tried to load typing library(TeachingDemos)
 
 But the message can´t find package TeachingDemos) occurs.
 I use versión
 R 2.9 on windows.
 
 Can you please guide me?
 
 Sorry¡¡¡
 
 
 
 
 
 2009/7/28, Petr PIKAL petr.pi...@precheza.cz:
 
  Hi
 
  r-help-boun...@r-project.org
 napsal dne 28.07.2009 09:55:11:
 
   Hi Greg I saw, read, the TeachingDemos you
 suggesttef but when run
  pairs2
   function on my R module says Can´t find
 function pairs2
  
   How can I load the module or function pairs2?
 
  Did you do
 
  library(TeachingDemos)?
 
  Regards
  Petr
 
 
  
   Thanks in advance for your help.
  
   You are the best.
  
   2009/7/27, Greg Snow greg.s...@imail.org:
   
Look at the pairs2 function in the
 TeachingDemos package.
   
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
   
   
 -Original Message-
 From: r-help-boun...@r-project.org
 [mailto:r-help-boun...@r-
 project.org] On Behalf Of Jose Narillos
 de Santos
 Sent: Monday, July 27, 2009 9:02 AM
 To: r-help@r-project.org
 Subject: [R] pairs plot

 Hi all,

 I want to plot trough pairs() plot a
 matrix with 4 columns. I want
  to
 make a
 trhee plot in a graph. Plotting pairs
 colum 2,3,4 on y axis and 1 on
  X
 axis.

 You mean (a plot with three graphs)
 ommitting the first pair with
 itself.
 And only the pairs with colum 1 with
 the other not all pairs.

 I. e. this matrix

 4177 289390 8740 17220
 3907 301510 8530 17550
 3975 316970 8640 17650
 3651 364220 9360 21420
 3031 387390 9960 23410
 2912 430180 11040 25820
 3018 499930 12240 27620
 2685 595010 13800 31670
 2884 661870 14760 37170

 Thanks in advance.

   
    [[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.
 
 
 
     [[alternative HTML version deleted]]
 
 
 -Inline Attachment Follows-
 
 __
 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.
 


  __
Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your 
favourite sites. Download it now
http://ca.toolbar.yahoo.com.

__
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] pairs plot

[Petr PIKAL]

r-help-boun...@r-project.org napsal dne 28.07.2009 15:39:03:

 
 Have you installed it first? 
 First: 
 install.packages(TeachingDemos)

Or if you have problems with correct setting through corporate network 
rules (like myself) you can download a zip (for Windows) version and unzip 
it to library subdirectory.

 Then:
 library(TeachingDemos)

shall be executed without problem

Regards
Petr


 
 
 --- On Tue, 7/28/09, Jose Narillos de Santos 
narillosdesan...@gmail.com wrote:
 
  From: Jose Narillos de Santos narillosdesan...@gmail.com
  Subject: Re: [R] pairs plot
  To: Petr PIKAL petr.pi...@precheza.cz, r-help@r-project.org, 
greg.s...@imail.org
  Received: Tuesday, July 28, 2009, 8:24 AM
  Hi,
  
  I tried to load typing library(TeachingDemos)
  
  But the message can´t find package TeachingDemos) occurs.
  I use versión
  R 2.9 on windows.
  
  Can you please guide me?
  
  Sorry¡¡¡
  
  
  
  
  
  2009/7/28, Petr PIKAL petr.pi...@precheza.cz:
  
   Hi
  
   r-help-boun...@r-project.org
  napsal dne 28.07.2009 09:55:11:
  
Hi Greg I saw, read, the TeachingDemos you
  suggesttef but when run
   pairs2
function on my R module says Can´t find
  function pairs2
   
How can I load the module or function pairs2?
  
   Did you do
  
   library(TeachingDemos)?
  
   Regards
   Petr
  
  
   
Thanks in advance for your help.
   
You are the best.
   
2009/7/27, Greg Snow greg.s...@imail.org:

 Look at the pairs2 function in the
  TeachingDemos package.

 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data Center
 Intermountain Healthcare
 greg.s...@imail.org
 801.408.8111


  -Original Message-
  From: r-help-boun...@r-project.org
  [mailto:r-help-boun...@r-
  project.org] On Behalf Of Jose Narillos
  de Santos
  Sent: Monday, July 27, 2009 9:02 AM
  To: r-help@r-project.org
  Subject: [R] pairs plot
 
  Hi all,
 
  I want to plot trough pairs() plot a
  matrix with 4 columns. I want
   to
  make a
  trhee plot in a graph. Plotting pairs
  colum 2,3,4 on y axis and 1 on
   X
  axis.
 
  You mean (a plot with three graphs)
  ommitting the first pair with
  itself.
  And only the pairs with colum 1 with
  the other not all pairs.
 
  I. e. this matrix
 
  4177 289390 8740 17220
  3907 301510 8530 17550
  3975 316970 8640 17650
  3651 364220 9360 21420
  3031 387390 9960 23410
  2912 430180 11040 25820
  3018 499930 12240 27620
  2685 595010 13800 31670
  2884 661870 14760 37170
 
  Thanks in advance.
 

 [[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.
  
  
  
  [[alternative HTML version deleted]]
  
  
  -Inline Attachment Follows-
  
  __
  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.
  
 
 
   __
 Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark 
your 
 favourite sites. Download it now
 http://ca.toolbar.yahoo.com.
 
 __
 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-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] pairs plot

[Jose Narillos de Santos]

Hi all,

I want to plot trough pairs() plot a matrix with 4 columns. I want to make a
trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X axis.

You mean (a plot with three graphs) ommitting the first pair with itself.
And only the pairs with colum 1 with the other not all pairs.

I. e. this matrix

4177 289390 8740 17220
3907 301510 8530 17550
3975 316970 8640 17650
3651 364220 9360 21420
3031 387390 9960 23410
2912 430180 11040 25820
3018 499930 12240 27620
2685 595010 13800 31670
2884 661870 14760 37170

Thanks in advance.

[[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] pairs plot

[Greg Snow]

Look at the pairs2 function in the TeachingDemos package.

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Jose Narillos de Santos
 Sent: Monday, July 27, 2009 9:02 AM
 To: r-help@r-project.org
 Subject: [R] pairs plot
 
 Hi all,
 
 I want to plot trough pairs() plot a matrix with 4 columns. I want to
 make a
 trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X
 axis.
 
 You mean (a plot with three graphs) ommitting the first pair with
 itself.
 And only the pairs with colum 1 with the other not all pairs.
 
 I. e. this matrix
 
 4177 289390 8740 17220
 3907 301510 8530 17550
 3975 316970 8640 17650
 3651 364220 9360 21420
 3031 387390 9960 23410
 2912 430180 11040 25820
 3018 499930 12240 27620
 2685 595010 13800 31670
 2884 661870 14760 37170
 
 Thanks in advance.
 
   [[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.

__
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] pairs of numbers

[emj83]

Hi,

I have two lists of numbers which are both 1,2,3,4.
I would like to combine pairs so that I have:
1,2
1,3
1,4
2,3
2,4
3,4.

I know that expand.grid() can give me all combinations of pairs. 

Any suggestions would be much appreciated.

Emma
-- 
View this message in context: 
http://www.nabble.com/pairs-of-numbers-tp22494116p22494116.html
Sent from the R help mailing list archive at Nabble.com.

__
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] pairs of numbers

[emj83]

I have solved my problem using:
 x-1:4
 x
[1] 1 2 3 4
 combn(x,2)
 [,1] [,2] [,3] [,4] [,5] [,6]
[1,]111223
[2,]234344

Thanks Emma


emj83 wrote:
 
 Hi,
 
 I have two lists of numbers which are both 1,2,3,4.
 I would like to combine pairs so that I have:
 1,2
 1,3
 1,4
 2,3
 2,4
 3,4.
 
 I know that expand.grid() can give me all combinations of pairs. 
 
 Any suggestions would be much appreciated.
 
 Emma
 

-- 
View this message in context: 
http://www.nabble.com/pairs-of-numbers-tp22494116p22494346.html
Sent from the R help mailing list archive at Nabble.com.

__
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] pairs() help - colour histograms on diagonal

[Duncan Murdoch]

Nathan S. Watson-Haigh wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I'd like to be able to colour histograms along the diagonal using the colours
stored in colnames(d):

  

d


 blackbluebrowncyan
1   0.96405751 -0.02964390 -0.060147424 -0.06460070
2  -0.03614607  0.95475444 -0.152382053 -0.07767974
3  -0.07095613 -0.05884884 -0.061289399 -0.06445973
4  -0.03708223 -0.05997624 -0.054044275 -0.08291373
5  -0.08877190 -0.07193658 -0.078598617 -0.08892916
6  -0.09294377 -0.05563854 -0.051405213 -0.08442332
7  -0.08431200 -0.01657793 -0.119773022 -0.07364633
8  -0.06105875 -0.05311773 -0.062928495 -0.06982507
9  -0.05757523 -0.02589045 -0.102312333 -0.05616588
10 -0.05092343 -0.03935830 -0.062069716 -0.05402492
11 -0.08057353 -0.12690058 -0.004248301 -0.06850326
12 -0.08052613 -0.04962747 -0.098955086 -0.06496541
13 -0.07901151 -0.07587651 -0.077401999  0.96525294
14 -0.07187448 -0.15431262  0.952982852 -0.06471004
15 -0.07230232 -0.13704876  0.032573081 -0.05040565



So I'd like the top-left histogram on the diagonal to be coloured black, then
the next one on the diagonal to be coloured blue etc. Is this possible?

  
Normally information about what is being plotted isn't passed to the 
panel function, and attributes of the columns are stripped off before 
passing, so this isn't easy.


If you want to do some ugly programming, you can look up the variable i 
in the sys.frame(2) environment; that will be the column number.  While 
you're at it, you might as well get the data too:  it's called x there. 
 For example,


d - data.frame(black=rnorm(100), blue=rnorm(100), brown=rnorm(100), 
cyan=rnorm(100))


panel.hist - function(x, ...) {
   # get some graphical parameter settings, and reset them on exit
   usr - par(usr)
   on.exit(par(usr))
  
   par(usr = c(usr[1:2], 0, 1.5) )
  
   # get a histogram of the data, but don't plot it - we just need to 
get some info from the histogram

   h - hist(x, plot = FALSE)
   breaks - h$breaks
   nB - length(breaks)
   y - h$counts; y - y/max(y)

   colnum - parent.frame(2)$i
   x - parent.frame(2)$x
   colour - colnames(x)[colnum] 
  
   rect(breaks[-nB], 0, breaks[-1], y, col=colour, ...)

}

pairs(d, upper.panel=panel.smooth, diag.panel=panel.hist)

Duncan Murdoch


Cheers,
Nathan

- --
- 
Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
- 

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (MingW32)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iEYEARECAAYFAkmHovYACgkQ9gTv6QYzVL5bUgCgw3EHQKS9WjO2AmtEks6x0Bh9
FLgAoIFpikJ903quFBaxQe5UVXAAbrnq
=XRan
-END PGP SIGNATURE-

__
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-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] pairs() help - colour histograms on diagonal

[Nathan S. Watson-Haigh]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I'd like to be able to colour histograms along the diagonal using the colours
stored in colnames(d):

 d
 blackbluebrowncyan
1   0.96405751 -0.02964390 -0.060147424 -0.06460070
2  -0.03614607  0.95475444 -0.152382053 -0.07767974
3  -0.07095613 -0.05884884 -0.061289399 -0.06445973
4  -0.03708223 -0.05997624 -0.054044275 -0.08291373
5  -0.08877190 -0.07193658 -0.078598617 -0.08892916
6  -0.09294377 -0.05563854 -0.051405213 -0.08442332
7  -0.08431200 -0.01657793 -0.119773022 -0.07364633
8  -0.06105875 -0.05311773 -0.062928495 -0.06982507
9  -0.05757523 -0.02589045 -0.102312333 -0.05616588
10 -0.05092343 -0.03935830 -0.062069716 -0.05402492
11 -0.08057353 -0.12690058 -0.004248301 -0.06850326
12 -0.08052613 -0.04962747 -0.098955086 -0.06496541
13 -0.07901151 -0.07587651 -0.077401999  0.96525294
14 -0.07187448 -0.15431262  0.952982852 -0.06471004
15 -0.07230232 -0.13704876  0.032573081 -0.05040565


panel.hist - function(x, ...) {
# get some graphical parameter settings, and reset them on exit
usr - par(usr)
on.exit(par(usr))

par(usr = c(usr[1:2], 0, 1.5) )

# get a histogram of the data, but don't plot it - we just need to get 
some
info from the histogram
h - hist(x, plot = FALSE)
breaks - h$breaks
nB - length(breaks)
y - h$counts; y - y/max(y)

rect(breaks[-nB], 0, breaks[-1], y, ...)
}

pairs(d, upper.panel=panel.smooth, diag.panel=panel.hist)

So I'd like the top-left histogram on the diagonal to be coloured black, then
the next one on the diagonal to be coloured blue etc. Is this possible?

Cheers,
Nathan

- --
- 
Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
- 

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (MingW32)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iEYEARECAAYFAkmHovYACgkQ9gTv6QYzVL5bUgCgw3EHQKS9WjO2AmtEks6x0Bh9
FLgAoIFpikJ903quFBaxQe5UVXAAbrnq
=XRan
-END PGP SIGNATURE-

__
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] pairs plots in R

[Antony Unwin]

If you want to do efficient exploratory data analysis on this kind of  
dataset, then interactive graphics with parallel coordinate plots  
(ipcp in iplots) should help.  Of course, it depends what you mean by  
large.  It might be worth looking at the book Graphics of Large  
Datasets for some ideas.

Antony Unwin
Professor of Computer-Oriented Statistics and Data Analysis,
Mathematics Institute,
University of Augsburg,
86135 Augsburg, Germany
Tel: + 49 821 5982218



 From: Sharma, Dhruv [EMAIL PROTECTED]
 Date: 19 October 2008 10:58:53 pm GMT+02:00
 To: r-help@r-project.org
 Subject: [R] pairs plots in R


 Hi,
  is there a way to take a data frame with 100+ columns and large  
 data set to do efficient exploratory analysis in R with pairs?

 I find using pairs on the whole matrix is slow and the resulting  
 matrix is tiny.

 Also the variable of interest for me is a binary var Y or N .

 Is there an efficient way to graphically view many variable  
 relationships that does not look teeny ?

 I could do pairs 10 at a time but this seems too brute force.

 thanks
 Dhruv

[[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] pairs plots in R

[Sharma, Dhruv]

Thanks Felix.

Regards,
Dhruv 

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Felix Andrews
Sent: Sunday, October 19, 2008 11:37 PM
To: Sharma, Dhruv
Cc: r-help@r-project.org
Subject: Re: [R] pairs plots in R


One idea:

if the primary variable of interest is a categorical (binary), I would rather 
look at univariate plots for each of your 100 variables, grouped by the primary 
one.

e.g.

library(latticeExtra)

marginal.plot(~ myBigDat, data = myBigData,
   groups = myBinaryVar, auto.key = TRUE,
   layout = c(4, 4))

(This is a convenient interface to lattice::densityplot and lattice::dotplot)

If you view 16 such densityplots per page, that still gives you 7 pages. You 
could use playwith() (from playwith package) to scroll through the pages.

-Felix

2008/10/20 Sharma, Dhruv [EMAIL PROTECTED]:
 Hi,
  is there a way to take a data frame with 100+ columns and large data set to 
 do efficient exploratory analysis in R with pairs?

 I find using pairs on the whole matrix is slow and the resulting matrix is 
 tiny.

 Also the variable of interest for me is a binary var Y or N .

 Is there an efficient way to graphically view many variable relationships 
 that does not look teeny ?

 I could do pairs 10 at a time but this seems too brute force.

 thanks
 Dhruv

[[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.




--
Felix Andrews / 安福立
http://www.neurofractal.org/felix/
3358 543D AAC6 22C2 D336  80D9 360B 72DD 3E4C F5D8
__
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] pairs plots in R

[Sharma, Dhruv]

thanks Antony.
 
regards,
Dhruv



From: Antony Unwin [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 20, 2008 7:00 AM
To: r-help@r-project.org
Cc: Sharma, Dhruv
Subject: Re: [R] pairs plots in R


If you want to do efficient exploratory data analysis on this kind of
dataset, then interactive graphics with parallel coordinate plots (ipcp
in iplots) should help.  Of course, it depends what you mean by large.
It might be worth looking at the book Graphics of Large Datasets for
some ideas.

Antony Unwin
Professor of Computer-Oriented Statistics and Data Analysis,
Mathematics Institute,
University of Augsburg, 
86135 Augsburg, Germany
Tel: + 49 821 5982218




From: Sharma, Dhruv [EMAIL PROTECTED]

Date: 19 October 2008 10:58:53 pm GMT+02:00

To: r-help@r-project.org

Subject: [R] pairs plots in R



Hi,
 is there a way to take a data frame with 100+ columns and large
data set to do efficient exploratory analysis in R with pairs?

I find using pairs on the whole matrix is slow and the resulting
matrix is tiny.

Also the variable of interest for me is a binary var Y or N .

Is there an efficient way to graphically view many variable
relationships that does not look teeny ?

I could do pairs 10 at a time but this seems too brute force.

thanks
Dhruv


[[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] pairs plots in R

[Felix Andrews]

One idea:

if the primary variable of interest is a categorical (binary), I would
rather look at univariate plots for each of your 100 variables,
grouped by the primary one.

e.g.

library(latticeExtra)

marginal.plot(~ myBigDat, data = myBigData,
   groups = myBinaryVar, auto.key = TRUE,
   layout = c(4, 4))

(This is a convenient interface to lattice::densityplot and lattice::dotplot)

If you view 16 such densityplots per page, that still gives you 7
pages. You could use playwith() (from playwith package) to scroll
through the pages.

-Felix

2008/10/20 Sharma, Dhruv [EMAIL PROTECTED]:
 Hi,
  is there a way to take a data frame with 100+ columns and large data set to 
 do efficient exploratory analysis in R with pairs?

 I find using pairs on the whole matrix is slow and the resulting matrix is 
 tiny.

 Also the variable of interest for me is a binary var Y or N .

 Is there an efficient way to graphically view many variable relationships 
 that does not look teeny ?

 I could do pairs 10 at a time but this seems too brute force.

 thanks
 Dhruv

[[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.




-- 
Felix Andrews / 安福立
http://www.neurofractal.org/felix/
3358 543D AAC6 22C2 D336  80D9 360B 72DD 3E4C F5D8

__
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] Pairs() function: selective changing of ylim; use of key

[David Afshartous]

All,

Two questions RE scatterplot matrices produced via pairs() function:

1) Is it possible to selectively change the ylim of one of the subplots?

2) Is a key allowed? I don't seem to be able to insert a manual key.

Code below:

dat = data.frame(Hour= rep(c(0:3), 4), Y1 = rnorm(16,1),
Y2 = rnorm(16,4),Drug = rep(c(P, D), each=4, 2) )

## this works:
pairs(dat, pch = 21, bg = c(red, green3)[unclass(dat$Drug)])

## this produces several warnings:
pairs(dat, pch = 21, bg = c(red, green3)[unclass(dat$Drug)],
key = list(space = top,  text = levels(dat$Drug), lines =
list(col=c(red, green3)), columns=2)  )

Cheers,
David

__
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] pairs diagram of qq plots?

[Dr. Stefan Reisner]

Hello everyone,
 
for some exploratory analysis I would like to compare the distribution of an
observable WERT pairwise between several samples identified by STICHPROBE
(which differ in size).
 
 str(stichproben_o1o4_20080327ff[c(STICHPROBE, WERT)])
'data.frame':   6087 obs. of  2 variables:
 $ STICHPROBE: num  9 9 2 2 7 3 2 3 8 6 ...
 $ WERT  : num  165 184 110 131 87 111 210 88 159 198 ...

A good way to compare two distributions is a Q-Q or Tukey mean-difference
(tmd) plot. I would like to arrange these qq or tmd plots in a matrix as the
pairs() function does.
 
Can pairs() be made to immediately produce tmd plots instead of plain
scatter plots, or will I have to do the tmd processing in a separate step
and only pass the such preprocessed xy data to pairs()?
 
Another problem is the representation of the data with respect to pairs().
My data.frame identifies the sample of each measurement in column
STICHPROBE. It does not have one column for each sample (note again that the
samples differ in size). From what I understand about pairs() it requires a
separate column for each variable. The reshape() function should be able to
change the representation but the best I can achieve is a wide dataframe
with multiple columns (as desired) but no rows:
 
 reshape(stichproben_o1o4_20080327ff[c(STICHPROBE, WERT)],
timevar=STICHPROBE, direction=wide)
 [1] WERT.9 WERT.2 WERT.7 WERT.3 WERT.8 WERT.6 WERT.1 WERT.4 WERT.0 WERT.5
0 rows (or 0-length row.names)
 
Best regards

Stefan

 

[[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.

[R] pairs, par(plt)

[Oliver Soong]

I'm having some confusion over the coordinate system after using
pairs.  I'm not interested in the content of the actual pairs plot,
although the number of pairs seems to matter a bit.  I'm purely
interested in knowing where my points will be plotted on the device.
However, after using pairs, the par information (omd, fig, plt, and
usr) don't reflect what points does.  For example:

pairs(iris[1:5])
par(xpd = NA)
points(0 - 0.01 * 1:100, 0 - 0.01 * 1:100)
points(0 - 0.01 * 1:100, 1 + 0.01 * 1:100)
points(1 + 0.01 * 1:100, 0 - 0.01 * 1:100)
points(1 + 0.01 * 1:100, 1 + 0.01 * 1:100)
par(c(omd, fig, plt, usr))

The resulting plot shows that the corners of the are approximately
0.05 user coordinate units from the boundaries of the plot region.
According to par, though, there is a margin around the plotting region
that is clearly not symmetric and does not correspond to around 0.05
units.

If we use pairs(iris[1:2]) and repeat the rest, the corners are now
0.02 user coordinate units.  par provides the same information as
before.

So:
1. How do I figure out where coordinates I give to points will display
on the figure?
2. More generally (for my own understanding), why does the par
information not do what I expect?  Do I have some fundamental
misunderstanding of the arrangement of plotting, figure, display, and
margin regions within the device?

I'm using R 2.5.1, and this behavior occurs on a fresh R console.

Thanks!

Oliver


-- 
Oliver Soong
Donald Bren School of Environmental Science  Management
University of California, Santa Barbara
Santa Barbara, CA 93106-5131
805-893-7044 (office)
610-291-9706 (cell)

__
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.