R help - Sep 2012 - Background color in a grid plot seems to interfere with plot()

Hi,

Why does the upper left panel (in the plot below) not have a gray background?

Cheers,

Marius


require(grid)
require(gridBase)

pdf(file="Rplot.pdf", width=8, height=8, onefile=FALSE)

## set up the grid layout
gl <- grid.layout(5, 5, widths=unit(c(1.8, 8, 0.8, 8, 0.8), "cm"),
		  heights=unit(c(0.8, 8, 0.8, 8, 1.5), "cm"))
if(FALSE) grid.show.layout(gl)
pushViewport(viewport(layout=gl))

## plot data
par. <- par(no.readonly=TRUE) # save plot settings
for(i in 1:2) { # rows
    i. <- if(i > 1) i+2 else i+1 # jumping over gaps
    for(j in 1:2) { # columns
        j. <- if(j > 1) j+2 else j+1 # jumping over gaps
        pushViewport(viewport(layout.pos.row=i., layout.pos.col=j.))
        grid.rect(gp=gpar(fill="gray90")) # background
        par(plt=gridPLT())
        ## plot
        plot(1:10, 1:10, log="y", xlab="",
ylab="",
             xaxt=if(i==2) "s" else "n", yaxt=if(j==1)
"s" else "n")
        par(new=TRUE) # to be run after first plot
        upViewport()
    }
}
par(par.)
dev.off()

Hi

On 24/09/12 09:36, Marius Hofert wrote:
> Hi,
>
> Why does the upper left panel (in the plot below) not have a gray
background?
That is a symptom of the conflict that occurs when the 'graphics' 
package and the 'grid' package both try to initialise a new page.
A good rule of thumb is to start a new page with 'graphics' first and 
THEN add 'grid' stuff ('grid' is better at sharing), so a minor 
adjustment to your code would be (#PAUL marks the changes) ...


pdf(file="Rplot.pdf", width=8, height=8, onefile=FALSE)
#PAUL
# Start (empty) new page with 'graphics'
plot.new()
## set up the grid layout
gl <- grid.layout(5, 5, widths=unit(c(1.8, 8, 0.8, 8, 0.8), "cm"),
		  heights=unit(c(0.8, 8, 0.8, 8, 1.5), "cm"))
pushViewport(viewport(layout=gl))
## plot data
par. <- par(no.readonly=TRUE) # save plot settings
for(i in 1:2) { # rows
     i. <- if(i > 1) i+2 else i+1 # jumping over gaps
     for(j in 1:2) { # columns
         j. <- if(j > 1) j+2 else j+1 # jumping over gaps
         pushViewport(viewport(layout.pos.row=i., layout.pos.col=j.))
         grid.rect(gp=gpar(fill="gray90")) # background
         par(plt=gridPLT())
         ## plot
         #PAUL
         # ALWAYS do this before each new 'graphics' plot
         par(new=TRUE)
         plot(1:10, 1:10, log="y", xlab="",
ylab="",
              xaxt=if(i==2) "s" else "n", yaxt=if(j==1)
"s" else "n")
         upViewport()
     }
}
par(par.)
dev.off()


Hope that helps.

Paul
> Cheers,
>
> Marius
>
>
> require(grid)
> require(gridBase)
>
> pdf(file="Rplot.pdf", width=8, height=8, onefile=FALSE)
>
> ## set up the grid layout
> gl <- grid.layout(5, 5, widths=unit(c(1.8, 8, 0.8, 8, 0.8),
"cm"),
> 		  heights=unit(c(0.8, 8, 0.8, 8, 1.5), "cm"))
> if(FALSE) grid.show.layout(gl)
> pushViewport(viewport(layout=gl))
>
> ## plot data
> par. <- par(no.readonly=TRUE) # save plot settings
> for(i in 1:2) { # rows
>      i. <- if(i > 1) i+2 else i+1 # jumping over gaps
>      for(j in 1:2) { # columns
>          j. <- if(j > 1) j+2 else j+1 # jumping over gaps
>          pushViewport(viewport(layout.pos.row=i., layout.pos.col=j.))
>          grid.rect(gp=gpar(fill="gray90")) # background
>          par(plt=gridPLT())
>          ## plot
>          plot(1:10, 1:10, log="y", xlab="",
ylab="",
>               xaxt=if(i==2) "s" else "n", yaxt=if(j==1)
"s" else "n")
>          par(new=TRUE) # to be run after first plot
>          upViewport()
>      }
> }
> par(par.)
> dev.off()
>
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-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/