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

[Marius Hofert]

Dear Paul,

Many thanks, that solved it.

Cheers,

Marius

Paul Murrell <p.murrell at auckland.ac.nz> writes:

> Hi
>
> On 25/09/2012 6:10 p.m., Marius Hofert wrote:
>> Dear Paul,
>>
>> Thanks. Redrawing the points solves it for the minimal example, but
>> what happens if you have plot(.., type="b") like below?
>
> You can use points(..., type="b")
>
> Paul
>
>> 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()
>>>>>>>>
>>>>>>>> ______________________________________________
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>>>>>>>> http://www.R-project.org/posting-guide.html and provide
>>>>>>>> commented, minimal, self-contained, reproducible code.
>>>>>>>>