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

[[alternative HTML version deleted]]

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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]]

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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]]

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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

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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

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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 wrote:

> 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.
>



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

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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

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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
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 


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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.

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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.

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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 Zhao
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 Zhao
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
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PLEASE  do read the posting guidehttp://www.R-project.org/posting-guide.html
and  provide commented, minimal, self-contained, reproducible code.

  __
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and  provide commented, minimal, self-contained, reprod

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

[Shi, Tao]

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 Zhao 
> 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 Zhao
> > 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]]
&g

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 Zhao
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]]

__
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PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

 

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

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 
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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] "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]]

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



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

Re: [R] pairs

[cindy Guo]

Thank you. I will check that.
Cindy

On Mon, Nov 16, 2009 at 1:45 PM, cls59  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.html
> and provide commented, minimal, self-contained, reproducible code.
>

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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  > 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 > > 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[tpair>1]
>> 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 > > 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[tpair>1]
>> 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[tpair>1], sum(tpair>1)/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

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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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 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 
> 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[tpair>1]
>> 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[tpair>1]
 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[tpair>1], sum(tpair>1)/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

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  > 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[tpair>1]
> 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  > 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[tpair>1]
> 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[tpair>1], sum(tpair>1)/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 c

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 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[tpair>1]
> 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 
>>> 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[tpair>1]
>>> 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[tpair>1], sum(tpair>1)/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-

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[tpair>1]
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 > 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[tpair>1]
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[tpair>1], sum(tpair>1)/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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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 > 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[tpair>1]
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[tpair>1], sum(tpair>1)/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

[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 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[tpair>1]
> 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[tpair>1], sum(tpair>1)/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
>
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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[tpair>1]
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[tpair>1], sum(tpair>1)/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

[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

[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  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.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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  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

[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

[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

[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 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 
 wrote:
> 
> > From: Jose Narillos de Santos 
> > Subject: Re: [R] pairs plot
> > To: "Petr PIKAL" , 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 :
> > >
> > > 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 :
> > > > >
> > > > > 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.

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  wrote:

> From: Jose Narillos de Santos 
> Subject: Re: [R] pairs plot
> To: "Petr PIKAL" , 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 :
> >
> > 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 :
> > > >
> > > > 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
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__
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 :
>
> 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 :
> > >
> > > 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

[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 :
> >
> > 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.

__
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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 :
>
> 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]]

__
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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.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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.

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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
- 

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FLgAoIFpikJ903quFBaxQe5UVXAAbrnq
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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: 

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]]

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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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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: 
> 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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 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
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