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

[Paul Murrell]

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()
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-help at 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.
>>>>>>>
>>>>>

-- 
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/