R help - Aug 2007 - Need help putting histograms on the diagonal of a splom plot

Hello,

I am in need of help in putting histograms on the diagonal of a plot 
produced with splom().

The plot matrix I am trying to produce is to have standard scatterplots 
in the upper-left triangle, contour plots in the lower-right triangle, 
and histograms on the diagonal. I have a function that does the first 
two, but the histograms on the diagonal has been beyond my ability.

Here is my function:

require(lattice)
require(MASS)
my.plot = function(data)
{
   splom( ~data
        , lower.panel=function(x,y, ...)
          {
            xy=kde2d(x,y)
            xy.tr=con2tr(xy)
            panel.contourplot( xy.tr$x
                             , xy.tr$y
                             , xy.tr$z
                             , subscripts=seq(nrow(xy.tr))
                             , contour=TRUE
                             , region=TRUE
                             , labels = FALSE
                             , col.regions = terrain.colors
                             )
          }
         , upper.panel=function(x,y, ...)
          {
            panel.grid(-1,-1)
            panel.xyplot(x,y, cex=0.5)
          }
        #, diag.panel=function(x, ...)
        #  {
        #    panel.histogram(x, ...)
        #  }
        )
}

It can be called, for example, with:

   my.plot(subset(iris, select = Sepal.Length:Petal.Width))

(the subset is necessary to get rid of a variable that is a factor; my 
function can not deal with factors).

I have commented out my best guess at the code needed to produce the 
histograms along the diagonal, which fails.

Any guidance would be greatly appreciated.

best regards,
Marc

On 8/30/07, Marc Paterno <paterno at fnal.gov>
wrote:
> Hello,
>
> I am in need of help in putting histograms on the diagonal of a plot
> produced with splom().
>
> The plot matrix I am trying to produce is to have standard scatterplots
> in the upper-left triangle, contour plots in the lower-right triangle,
> and histograms on the diagonal. I have a function that does the first
> two, but the histograms on the diagonal has been beyond my ability.
>
> Here is my function:
>
> require(lattice)
> require(MASS)
> my.plot = function(data)
> {
>    splom( ~data
>         , lower.panel=function(x,y, ...)
>           {
>             xy=kde2d(x,y)
>             xy.tr=con2tr(xy)
>             panel.contourplot( xy.tr$x
>                              , xy.tr$y
>                              , xy.tr$z
>                              , subscripts=seq(nrow(xy.tr))
>                              , contour=TRUE
>                              , region=TRUE
>                              , labels = FALSE
>                              , col.regions = terrain.colors
>                              )
>           }
>          , upper.panel=function(x,y, ...)
>           {
>             panel.grid(-1,-1)
>             panel.xyplot(x,y, cex=0.5)
>           }
>         #, diag.panel=function(x, ...)
>         #  {
>         #    panel.histogram(x, ...)
>         #  }
>         )
> }
>
> It can be called, for example, with:
>
>    my.plot(subset(iris, select = Sepal.Length:Petal.Width))
>
> (the subset is necessary to get rid of a variable that is a factor; my
> function can not deal with factors).
>
> I have commented out my best guess at the code needed to produce the
> histograms along the diagonal, which fails.
Well, basically the y-axis range of the diagonal panels are not right.
What you want is simpler if you are happy with a density estimate:


my.plot = function(data)
{
  splom( ~data
       #, lower.panel=...
       #, upper.panel=...
       , diag.panel = function(x, ...)
         {
             yrng <- current.panel.limits()$ylim
             d <- density(x)
             d$y <- with(d, yrng[1] + 0.95 * diff(yrng) * y / max(y) )
             panel.lines(d)
         })
}

my.plot(iris[1:4])

For a histogram, things are a bit more complicated, but still easy enough:

my.plot = function(data)
{
  splom( ~data
       #, lower.panel=...
       #, upper.panel=...
       , diag.panel = function(x, ...)
         {
             yrng <- current.panel.limits()$ylim
             d <- density(x)
             d$y <- with(d, yrng[1] + 0.95 * diff(yrng) * y / max(y) )
             panel.lines(d)
         })
}

-Deepayan

Hello,

I think the histograms may have been unintentionally omitted from the 
examples below. Borrowing from a couple of sources, here's a function to 
get the histograms instead of the density plot:

panel.hist.splom<-function(x, ...)

     {

         yrng <- current.panel.limits()$ylim

         h <- hist(x, plot = FALSE)

         breaks <- h$breaks; nB <- length(breaks)

         y <- h$counts; y <- yrng[1] + 0.95 * diff(yrng) * y / max(y)

         panel.rect(breaks[-nB], yrng[1], breaks[-1], y, col="cyan",
...)

     }


-Ben



From: Deepayan Sarkar <deepayan.sarkar_at_gmail.com 
<mailto:deepayan.sarkar_at_gmail.com?Subject=Re:%20%5BR%5D%20Need%20help%20putting%20histograms%20on%20the%20diagonal%20of%20a%20splom%20plot>>

Date: Fri, 31 Aug 2007 14:02:27 -0700

On 8/30/07, Marc Paterno <paterno_at_fnal.gov> wrote:
 > Hello, 
<http://tolstoy.newcastle.edu.au/R/e2/help/07/08/24539.html#24614qlink1>
/> /
/> I am in need of help in putting histograms on the diagonal of a plot /
/> produced with splom(). /
/> /
/> The plot matrix I am trying to produce is to have standard scatterplots /
/> in the upper-left triangle, contour plots in the lower-right triangle, /
/> and histograms on the diagonal. I have a function that does the first /
/> two, but the histograms on the diagonal has been beyond my ability. /
/> /
/> Here is my function: /
/> /
/> require(lattice) /
/> require(MASS) /
/> my.plot = function(data) /
/> { /
/> splom( ~data /
/> , lower.panel=function(x,y, ...) /
/> { /
/> xy=kde2d(x,y) /
/> xy.tr=con2tr(xy) /
/> panel.contourplot( xy.tr$x /
/> , xy.tr$y /
/> , xy.tr$z /
/> , subscripts=seq(nrow(xy.tr)) /
/> , contour=TRUE /
/> , region=TRUE /
/> , labels = FALSE /
/> , col.regions = terrain.colors /
/> ) /
/> } /
/> , upper.panel=function(x,y, ...) /
/> { /
/> panel.grid(-1,-1) /
/> panel.xyplot(x,y, cex=0.5) /
/> } /
/> #, diag.panel=function(x, ...) /
/> # { /
/> # panel.histogram(x, ...) /
/> # } /
/> ) /
/> } /
/> /
/> It can be called, for example, with: /
/> /
/> my.plot(subset(iris, select = Sepal.Length:Petal.Width)) /
/> /
/> (the subset is necessary to get rid of a variable that is a factor; my /
/> function can not deal with factors). /
/> /
/> I have commented out my best guess at the code needed to produce the /
/> histograms along the diagonal, which fails. /

Well, basically the y-axis range of the diagonal panels are not right. 
What you want is simpler if you are happy with a density estimate:

my.plot = function(data)
{
  splom( ~data

       #, lower.panel=...
       #, upper.panel=...
       , diag.panel = function(x, ...)
         {
             yrng <- current.panel.limits()$ylim
             d <- density(x)
             d$y <- with(d, yrng[1] + 0.95 * diff(yrng) * y / max(y) )
             panel.lines(d)
         })


}

my.plot(iris[1:4])

For a histogram, things are a bit more complicated, but still easy enough:

my.plot = function(data)
{
  splom( ~data

       #, lower.panel=...
       #, upper.panel=...
       , diag.panel = function(x, ...)
         {
             yrng <- current.panel.limits()$ylim
             d <- density(x)
             d$y <- with(d, yrng[1] + 0.95 * diff(yrng) * y / max(y) )
             panel.lines(d)
         })


}

-Deepayan

-- 
Benjamin Barnes, MEM

Doctoral Student
Department of Environmental Epidemiology

German Cancer Research Center
Im Neuenheimer Feld 280
D-69120 Heidelberg