Background color in a grid plot seems to interfere with plot()

Dear Paul,

Thanks. Redrawing the points solves it for the minimal example, but
what happens if you have plot(.., type="b") like below?

Actually, originally I wanted to use just grid (without mixing it
with base graphics), but I couldn't find an equivalent for plot(..,
type="b"). Also, later on, I would like to use eaxis() to draw nice
y-axes in log-scale. I guess that's easier with gridBase then.

Cheers,

Marius



require(grid) require(gridBase)

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

## set up the grid layout plot.new() # start (empty) new page with
'graphics' 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(col=NA, fill="gray90")) # background
par(plt=gridPLT()) ## plot par(new=TRUE) # always do this before each
new 'graphics' plot plot(runif(5), runif(5), type="b", log="y",
xlab="", ylab="", frame.plot=FALSE, xaxt="n", yaxt="n")
grid(col="white", lty="solid", lwd=1.6, equilogs=FALSE) # background
grid upViewport() } } par(par.) dev.off()


Paul Murrell<paul at stat.auckland.ac.nz>  writes:

Hi

On 25/09/12 11:50, Marius Hofert wrote:

Dear Paul,

Thanks for helping. Is there a way to call grid() first? The
problem seems to be that everything drawn before grid() is
overplotted.

No, but you can redraw the points ...

require(grid) require(gridBase)

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

## set up the grid layout plot.new() # start (empty) new page with
'graphics' 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(col=NA, fill="gray90")) #
background par(plt=gridPLT()) ## plot par(new=TRUE) # always do
this before each new 'graphics' plot plot(1:5, if(i==1&&  j==2)
c(1, 1, 2, 3, 1) else 1:5, log="y", xlab="", ylab="",
frame.plot=FALSE, xaxt="n", yaxt="n") # background grid
grid(col="white", lty="solid", lwd=1.6, equilogs=FALSE) points(1:5,
if(i==1&&  j==2) c(1, 1, 2, 3, 1) else 1:5) upViewport() } }
par(par.) dev.off()

Paul

Cheers,

Marius



require(grid) require(gridBase)

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

## set up the grid layout plot.new() # start (empty) new page
with 'graphics' 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(col=NA, fill="gray90")) #
background par(plt=gridPLT()) ## plot par(new=TRUE) # always do
this before each new 'graphics' plot plot(1:5, if(i==1&&  j==2)
c(1, 1, 2, 3, 1) else 1:5, log="y", xlab="", ylab="",
frame.plot=FALSE, xaxt="n", yaxt="n") grid(col="white",
lty="solid", lwd=1.6, equilogs=FALSE) # background grid
upViewport() } } par(par.) dev.off()


Paul Murrell<paul at stat.auckland.ac.nz>  writes:

Hi

On 24/09/12 18:06, Marius Hofert wrote:

Dear Paul,

Thank you for helping. This works great.

I then tried to put in a grid (via grid()). Why does that
fail?

Because grid() is used to add lines to an existing plot;  just
put the grid() call AFTER the plot() call and it should work
ok.

Paul

Cheers,

Marius


require(grid) require(gridBase)

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

## set up the grid layout plot.new() # start (empty) new page
with 'graphics' 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 par(new=TRUE) # always do this
before each new 'graphics' plot grid(col=1) 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()



Paul Murrell<paul at stat.auckland.ac.nz>  writes:

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()