R devel - Jun 2009 - Problems with plot and Quartz device (PR#13744)

Full_Name: Thomas Richardson
Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395)
OS: 10.4.11
Submission from: (NULL) (216.254.15.72)



I have encountered a problem with points in scatterplots disappearing in a
quartz window when it is re-sized (to make it larger).

I am constructing an 8x12 matrix of scatterplots each containing approx 600
points.
In order to get them in the window I remove the axes etc.,

quartz()
par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0))
for(i in 1:8){ # Row counter
for(j in 1:12){ # Col counter		
plot(rna$red[(rna$row==levels(rna$row[i])&(rna$col==j)],
     rna$tof[(rna$row==levels(rna$row[i])&(rna$col==j)],
    
xlab="tof",ylab="green",xaxt="n",yaxt="n",
     ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".")
}
}

Here is the problem:  how many data points actually appear in the quartz window
on my screen is highly sensitive to the width and height specified. If I specify
a different width and height for the quartz window e.g.
quartz(width=8,height=8), OR if I resize the window with the cursor then points
disappear in certain (x-axis) ranges across all the plots in some columns. These
bands in which points disappear are the same for all plots in a given column,
and can be very wide - making a lot of points disappear. 

(The visual effect is to make it look as if there are clearly defined vertical
white lines going across the scatterplots - though the black lines enclosing
each plot are not broken).

The problem seems to disappear with other plotting symbols e.g.
pch="+" (but
then I end up with crowded plots). So I guess it might be related to the
"special treatment" of "." described on help(points) ??
---
Value pch="." (equivalently pch = 46) is handled specially. It is a
rectangle of
side 0.01 inch (scaled by cex).
---

I find this behaviour unnerving: the (resized) plots made it look as if there
was a lot of structure in the data, but on closer inspection it turned out to be
entirely a consequence of the quartz device and plot function!

I can't imagine that this behaviour is intended - even if it were intended
to
suppress points (like some axis labels) - it seems strange that enlarging the
window makes points disappear. (I also tried setting dpi=72 in quartz(), but
this did not fix the problem).

Thanks in advance.

Thomas

------------------------------------------------------
 sessionInfo()
R version 2.9.0 (2009-04-17) 
i386-apple-darwin8.11.1 

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Thomas,

rna is not defined in R, can you, please, supply a reproducible  
example? From your description I think I know roughly what's going on  
(Quartz attempts to snap rectangles on pixel boundaries to prevent  
malignant anti-aliasing effects in image plots and this may somehow  
interact with pch='.' since Quartz has no way of knowing that those  
rectangles are supposed to be glyphs), but I cannot reproduce it.

Thanks,
Simon


On Jun 3, 2009, at 4:45 , tsr at stat.washington.edu wrote:
> Full_Name: Thomas Richardson
> Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395)
> OS: 10.4.11
> Submission from: (NULL) (216.254.15.72)
>
>
>
> I have encountered a problem with points in scatterplots  
> disappearing in a
> quartz window when it is re-sized (to make it larger).
>
> I am constructing an 8x12 matrix of scatterplots each containing  
> approx 600
> points.
> In order to get them in the window I remove the axes etc.,
>
> quartz()
> par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0))
> for(i in 1:8){ # Row counter
> for(j in 1:12){ # Col counter		
> plot(rna$red[(rna$row==levels(rna$row[i])&(rna$col==j)],
>     rna$tof[(rna$row==levels(rna$row[i])&(rna$col==j)],
>    
xlab="tof",ylab="green",xaxt="n",yaxt="n",
>     ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".")
> }
> }
>
> Here is the problem:  how many data points actually appear in the  
> quartz window
> on my screen is highly sensitive to the width and height specified.  
> If I specify
> a different width and height for the quartz window e.g.
> quartz(width=8,height=8), OR if I resize the window with the cursor  
> then points
> disappear in certain (x-axis) ranges across all the plots in some  
> columns. These
> bands in which points disappear are the same for all plots in a  
> given column,
> and can be very wide - making a lot of points disappear.
>
> (The visual effect is to make it look as if there are clearly  
> defined vertical
> white lines going across the scatterplots - though the black lines  
> enclosing
> each plot are not broken).
>
> The problem seems to disappear with other plotting symbols e.g.  
> pch="+" (but
> then I end up with crowded plots). So I guess it might be related to  
> the
> "special treatment" of "." described on help(points) ??
> ---
> Value pch="." (equivalently pch = 46) is handled specially. It is
a
> rectangle of
> side 0.01 inch (scaled by cex).
> ---
>
> I find this behaviour unnerving: the (resized) plots made it look as  
> if there
> was a lot of structure in the data, but on closer inspection it  
> turned out to be
> entirely a consequence of the quartz device and plot function!
>
> I can't imagine that this behaviour is intended - even if it were  
> intended to
> suppress points (like some axis labels) - it seems strange that  
> enlarging the
> window makes points disappear. (I also tried setting dpi=72 in  
> quartz(), but
> this did not fix the problem).
>
> Thanks in advance.
>
> Thomas
>
> ------------------------------------------------------
> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

On Jun 3, 2009, at 4:45 , tsr at stat.washington.edu wrote:
> Full_Name: Thomas Richardson
> Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395)
> OS: 10.4.11
> Submission from: (NULL) (216.254.15.72)
>
>
>
> I have encountered a problem with points in scatterplots  
> disappearing in a
> quartz window when it is re-sized (to make it larger).
>
> I am constructing an 8x12 matrix of scatterplots each containing  
> approx 600
> points.
> In order to get them in the window I remove the axes etc.,
>
> quartz()
> par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0))
> for(i in 1:8){ # Row counter
> for(j in 1:12){ # Col counter		
> plot(rna$red[(rna$row==levels(rna$row[i])&(rna$col==j)],
>     rna$tof[(rna$row==levels(rna$row[i])&(rna$col==j)],
>    
xlab="tof",ylab="green",xaxt="n",yaxt="n",
>     ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".")
> }
> }
>
> Here is the problem:  how many data points actually appear in the  
> quartz window
> on my screen is highly sensitive to the width and height specified.  
> If I specify
> a different width and height for the quartz window e.g.
> quartz(width=8,height=8), OR if I resize the window with the cursor  
> then points
> disappear in certain (x-axis) ranges across all the plots in some  
> columns. These
> bands in which points disappear are the same for all plots in a  
> given column,
> and can be very wide - making a lot of points disappear.
>
> (The visual effect is to make it look as if there are clearly  
> defined vertical
> white lines going across the scatterplots - though the black lines  
> enclosing
> each plot are not broken).
>
> The problem seems to disappear with other plotting symbols e.g.  
> pch="+" (but
> then I end up with crowded plots).

BTW: you may want to use something like pch=19, cex=0.1 (and maybe add  
some alpha to get a quick density estimation).

Cheers,
S

> So I guess it might be related to the
> "special treatment" of "." described on help(points) ??
> ---
> Value pch="." (equivalently pch = 46) is handled specially. It is
a
> rectangle of
> side 0.01 inch (scaled by cex).
> ---
>
> I find this behaviour unnerving: the (resized) plots made it look as  
> if there
> was a lot of structure in the data, but on closer inspection it  
> turned out to be
> entirely a consequence of the quartz device and plot function!
>
> I can't imagine that this behaviour is intended - even if it were  
> intended to
> suppress points (like some axis labels) - it seems strange that  
> enlarging the
> window makes points disappear. (I also tried setting dpi=72 in  
> quartz(), but
> this did not fix the problem).
>
> Thanks in advance.
>
> Thomas
>
> ------------------------------------------------------
> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>