[R] Surprise when mapping matrix to image

[Jim Brennan]

I was also surprised by the image orientation this summer and used the
"easy" fix of matrix manipulation. There is however another issue and that
is when you start flipping around the matrix, orders etc. and for the case
you want to have sensibly labeled axes, you may have to use the axis
commands etc. which is also easy, but accumulation of easy fixes can be
tedious so there is perhaps some argument for yet another new documentation
submission. Maybe a method for easily changing the orientation in image
could be added.

Jim
----- Original Message -----
From: "A.J. Rossini" <rossini at blindglobe.net>
To: <r-help at stat.math.ethz.ch>
Sent: Thursday, August 26, 2004 7:11 PM
Subject: Re: [R] Surprise when mapping matrix to image


>
> I think I'd have to respectfully disagree with both Brian and
> Deepayan, as to whether it should be obvious.  It is reasonable
> (principle of least suprise) to expect orientation of the plot to
> match the print order of the matrix.  I would have expected Brian's
> one-liner to be in the help page, with a notice.  It's a not-so-rare
> activity, being a general matrix visualization that is commonly used
> in certain areas of science (whether it ought to be commonly used is a
> separate question).
>
> While "heatmap" might've been perhaps a better pointer, but it doesn't
> seem to do the "right" thing, either.  I.e.
>
> myTemp <- matrix(c(1,2,3,3,2,3),nrow=2)
> heatmap(myTemp,Rowv=NA,Colv=NA)
>
> doesn't look right to me (R Version 1.9.1  (2004-06-21))
>
> I see the "pixmap/bitmap" issue as a bit of a red herring, in this
> case.
>
> best,
> -tony
>
> p.s. I seem to get bit by this about once a year for the last few,
> hence why I'm speaking up.
>
>
>
>
>
>
>
>
> Deepayan Sarkar <deepayan at cs.wisc.edu> writes:
>
> > Quoting "Glynn, Earl" <EFG at Stowers-Institute.org>:
> >
> >> Prof Ripley:
> >>
> >> Thank you for your prompt reply.
> >>
> >> > It's pure convention: see below.
> >> >
> >> > Did you try reading the help for image?  You don't seem to
> >> > understand it
> >> > if you actually did.  It seems you are looking for
> >> >
> >> >  image(t(x)[ncol(x):1, ])
> >>
> >> I think you guys are too close to "R" to understand how hard it is to
> >> use sometimes.  What may be blatantly obvious to you is quite a problem
> >> especially to beginners.  Some of us may be beginners to R, but we know
> >> math, science, programming, and how to solve problems with other tools
> >> and languages.
> >>
> >> I re-read the guidelines before posting fearing condemnation.
> >>
> >> Before posting I searched the online R-help Google interface with
> >> keywords "image", "flip", "rotate".  A discussion from 1998 touched on
> >> this issue but I was hoping that this was deemed a "bug" at some point
> >> and fixed -- or had an easy workaround, like some parameter I was
> >> missing.
> >>
> >> I read the "?image" help before posting. Was the part I didn't
> >> understand buried in this "note"?
> >>
> >>      "Based on a function by Thomas Lumley tlumley at u.washington.edu."
> >
> > You seem to be thinking that Prof Ripley's solution had something to do
with
> > image(). It doesn't, it has to do with manipulating a matrix. image()
> > visualizes a matrix in a particular and well-defined way. You want your
matrix
> > to be shown in a different way, and one (simple) way of doing that is to
> > convert your matrix into a different matrix, on which calling image
would give
> > you what you want. Why would this be explained in ?image ? This is basic
R.
> >
> > More generally, I think your frustration is caused by your expectation
that a
> > matrix object should behave like a bitmap image. It doesn't. If you want
work
> > with images, use the pixmap package.
> >
> > Deepayan
> >
> > ______________________________________________
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> > PLEASE do read the posting guide!
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> >
>
> --
> Anthony Rossini     Research Associate Professor
> rossini at u.washington.edu            http://www.analytics.washington.edu/
> Biomedical and Health Informatics   University of Washington
> Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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