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 , t...@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
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