[R] About plot graphs
Greg Snow
Greg.Snow at imail.org
Sat Aug 28 20:58:12 CEST 2010
Gavin gave some problems with relying attaching data, here is another example, somewhat artificial, but not unrealistic (I had similar to this happen to me before I learned better):
attach(women)
# do some stuff
library(lattice)
attach(singer)
# do some more stuff
# now we want to go back and look at the women data
plot(weight,height)
#or even worse
detach()
attach(singer[1:15,])
plot(weight,height)
# what conclusions do we draw from the plot?
detach()
detach()
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Stephen Liu
> Sent: Friday, August 27, 2010 11:14 PM
> To: gavin.simpson at ucl.ac.uk
> Cc: r-help at r-project.org
> Subject: Re: [R] About plot graphs
>
> Hi Gavin,
>
>
> Thanks for your advice and the examples explaining plotting settings.
>
> The steps on your examples work on my test.
>
>
> > 2) Don't attach() things, you are asking for trouble
>
> > If a function has a formula method (which plot does) then use it like
> > this: plot(Draft_No. ~ Day_of_year, data = Test01)
>
> > If the function doesn't have a formula method, then wrap it in a
> > with()
> > call:
>
> > with(Test01, plot(Day_of_year, Draft_No.))
>
> > No need for attach.
>
>
> Noted and thanks. What will be the problem caused by "attach()"?
>
>
> > dev.new(height = 6, width = 12)
> > layout(matrix(1:2, ncol = 2))
> > op <- par(pty = "s") ## this is the important bit
> > plot(runif(100), rnorm(100))
> > plot(runif(100), rnorm(100), col = "red")
> > par(op) ## now reset the pars
> > layout(1)
>
> What is the function of layout(1) ? Tks
>
>
> B.R.
> satimis
>
>
>
>
> ----- Original Message ----
> From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
> To: Stephen Liu <satimis at yahoo.com>
> Cc: "r-help at r-project.org" <r-help at r-project.org>
> Sent: Fri, August 27, 2010 5:38:40 PM
> Subject: Re: [R] About plot graphs
>
> On Fri, 2010-08-27 at 02:05 -0700, Stephen Liu wrote:
> > Hi Gavin,
> >
> > Thanks for your advice which works for me.
> >
> >
> > (rectangular window)
> > dev.new(height = 6, width = 12)
> > layout(matrix(1:2, nrow=1))
> > plot(Test01$Day_of_year, Test01$Draft_No.)
> > attach(Test01)
> > plot(Day_of_year,Draft_No.)
>
> 1) I can't reproduce this; where/what is Test01? But don;t bother
> sending, see my example below
> 2) Don't attach() things, you are asking for trouble
>
> If a function has a formula method (which plot does) then use it like
> this: plot(Draft_No. ~ Day_of_year, data = Test01)
>
> If the function doesn't have a formula method, then wrap it in a with()
> call:
>
> with(Test01, plot(Day_of_year, Draft_No.))
>
> No need for attach.
>
> >
> > (rectangular window in vertical position)
> > dev.new(height = 12, width = 4)
> > layout(matrix(1:2, nrow=2))
> > plot(Test01$Day_of_year, Test01$Draft_No.)
> > plot(Day_of_year,Draft_No.)
> >
> > (height = 12, width = 6) can't work. The graphs plotted are
> distorted off
> > square shape. I must reduce "width = 4"
> >
> > Why? TIA
>
> Because you don't appreciate that the dimensions of the device are not
> the same as the dimensions of the plotting region *on* the device. Most
> notably, the margins on the device are given by par("mar") for example
> and are not square:
>
> > par("mar")
> [1] 5.1 4.1 4.1 2.1
>
> So more space is set aside on the bottom then anywhere else, and the
> margin on the right is quite small.
>
> You have already been provided with an answer that you dismissed
> because
> you didn't appear to appreciate what you were being told.
>
> Compare this:
>
> dev.new(height = 6, width = 12)
> layout(matrix(1:2, ncol = 2))
> plot(runif(100), rnorm(100))
> plot(runif(100), rnorm(100), col = "red")
> layout(1)
>
> with this:
>
> dev.new(height = 6, width = 12)
> layout(matrix(1:2, ncol = 2))
> op <- par(pty = "s") ## this is the important bit
> plot(runif(100), rnorm(100))
> plot(runif(100), rnorm(100), col = "red")
> par(op) ## now reset the pars
> layout(1)
>
> So now the regions are square, we have the asymmetric margins like all
> R
> plots and we have drawn this on a device that has ~ appropriate
> dimensions.
>
> If you want to fiddle more with this, then you'll need to make the
> margins equal, but you don't want to do that really as you need more
> space in certain areas to accommodate axis labels and tick labels etc.
>
> For the vertical one, this works for me, though note that because of
> the
> margins, pty = "s" is making the individual plotting regions smaller to
> respect the square plotting region you asked for.
>
> dev.new(height = 12, width = 6)
> layout(matrix(1:2, ncol = 1))
> op <- par(pty = "s") ## this is the important bit
> plot(runif(100), rnorm(100))
> plot(runif(100), rnorm(100), col = "red")
> par(op) ## now reset the pars
> layout(1)
>
> This is because you have 5.1 plus 4.1 lines of margin in the vertical
> direction per plot (so 18.4 lines in total) versus 4.1 + 2.1 = 6.2
> lines
> of margin in the horizontal direction. So to make the plots square,
> the
> horizontal direction is restricted. If we take a bit of space out of
> the
> top/bottom margins, things improve (note I reduce the height as it
> doesn't fit properly on my monitor):
>
> dev.new(height = 10, width = 5)
> layout(matrix(1:2, ncol = 1))
> op <- par(pty = "s", mar = c(4,4,3,2) + 0.1)
> plot(runif(100), rnorm(100))
> plot(runif(100), rnorm(100), col = "red")
> par(op) ## now reset the pars
> layout(1)
>
> So as we reduce the vertical space required for margins, the square
> panels start to occupy more and more of the total device.
>
> Finally, notice how I provided examples that *you*, *me* and *anyone*
> else on the list can use to test behaviour/point out problems. Ths is
> what we call a reproducible example. If you want help without going
> round the houses (lots of dead ends), specifying an example like I did
> (your problem is not with *your* data but with using the R functions,
> so
> who cares what the data are?) above allows us very quickly to home in
> on
> the problem you have.
>
> > Looked at ?dev.new
> > can't resolve.
> >
> > Whether use another command such as;
> > dev.cur()
> > dev.list()
> > dev.next(which = dev.cur())
> > dev.prev(which = dev.cur())
> > dev.off(which = dev.cur())
> > dev.set(which = dev.next())
> > graphics.off()
> > ?
>
> If you had read ?dev.new (and understood it), you would know that those
> commands you list can't possibly help.
>
> HTH
>
> G
>
> >
> >
> > B.R.
> > Stephen L
> >
> >
> >
> >
> > ----- Original Message ----
> > From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
> > To: Stephen Liu <satimis at yahoo.com>
> > Cc: "r-help at r-project.org" <r-help at r-project.org>
> > Sent: Fri, August 27, 2010 4:21:13 PM
> > Subject: Re: [R] About plot graphs
> >
> > On Thu, 2010-08-26 at 21:01 -0700, Stephen Liu wrote:
> > > Hi Greg,
> > <snip />
> > > > windows(width=12, height=6)
> > > Error: could not find function "windows"
> >
> > So you aren't on Windows then... Hence why the posting guide asks for
> > sessionInfo() details; sometimes it matters.
> >
> > Anyway, a OS independent way of doing this is to use dev.new() and
> pass
> > along the arguments you would have provided to the device via e.g.
> > windows():
> >
> > dev.new(height = 6, width = 12)
> >
> > HTH
> >
> > G
> >
> > >
> > > > ?windows
> > > No documentation for 'windows' in specified packages and libraries:
> > > you could try '??windows'
> > >
> > >
> > > > window(width=12, height=6)
> > > Error in hasTsp(x) :
> > > element 1 is empty;
> > > the part of the args list of 'attr' being evaluated was:
> > > (x, "tsp")
> > >
> > >
> > > > ?window
> > > window {stats}
> > > http://stat.ethz.ch/R-manual/R-devel/library/stats/html/window.html
> > >
> > > window package:stats R
> Documentation
> > >
> > > Time Windows
> > >
> > > Description:
> > >
> > > ‘window’ is a generic function which extracts the subset of
> the
> > > object ‘x’ observed between the times ‘start’ and ‘end’. If a
> > > frequency is specified, the series is then re-sampled at the
> new
> > > frequency.
> > >
> > >
> > > > window(layout(matrix(1:2, nrow=1), width=12, height=6))
> > > [1] 2
> > > attr(,"tsp")
> > > [1] 1 1 1
> > >
> > >
> > > Still pop up a square window
> > >
> > >
> > > B.R
> > > Stephen L
> > >
> > >
> > >
> > >
> > >
> > > ----- Original Message ----
> > > From: Greg Snow <Greg.Snow at imail.org>
> > > To: Stephen Liu <satimis at yahoo.com>; "r-help at r-project.org"
> > > <r-help at r-project.org>
> > > Sent: Fri, August 27, 2010 10:51:21 AM
> > > Subject: RE: [R] About plot graphs
> > >
> > > When you run any graphics command (layout in this case) and there
> is not a
> > > current graphics device (more technically only the null device)
> then a
> >default
> >
> >
> > > graphics device is opened, that is what you are seeing. What you
> need to do
>
> > > instead is open the device yourself before calling layout. Which
> device that
> >
> > >is
> > >
> > > depends greatly on information that the posting guide strongly
> suggests that
>
> > >you
> > >
> > > provide (another hint).
> > >
> > > One possibility is:
> > >
> > > > windows(width=12, height=6)
> > >
> > > Followed by layout and the plotting commands. But whether that
> will work on
>
> > > your machine or not is still a bit of a mystery.
> > >
> > > --
> > > Gregory (Greg) L. Snow Ph.D.
> > > Statistical Data Center
> > > Intermountain Healthcare
> > > greg.snow at imail.org
> > > 801.408.8111
> > >
> > >
> > > > -----Original Message-----
> > > > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> > > > project.org] On Behalf Of Stephen Liu
> > > > Sent: Thursday, August 26, 2010 8:02 PM
> > > > To: r-help at r-project.org
> > > > Subject: Re: [R] About plot graphs
> > > >
> > > > Hi Greg,
> > > >
> > > > Thanks for your advice.
> > > >
> > > > I'm not prepared altering the shape of the graphs to be plotted.
> What
> > > > I'm
> > > > trying to do is to pop up a rectangle layout window with
> following
> > > > command.
> > > >
> > > > The command;
> > > > layout(matrix(1:2, nrow=1))
> > > >
> > > > pop up a square window. What I need is a rectangular window for
> the
> > > > graphs to
> > > > be plotted. Otherwise the graphs are squeezed changing shape.
> > > >
> > > > I looked at ?layout but can't resolve how to make it. Can you
> help?
> > > > TIA
> > > >
> > > > B.R.
> > > > Stephen L
> > > >
> > > >
> > > >
> > > >
> > > > ----- Original Message ----
> > > > From: Greg Snow <Greg.Snow at imail.org>
> > > > To: Stephen Liu <satimis at yahoo.com>; "r-help at r-project.org"
> > > > <r-help at r-project.org>
> > > > Sent: Fri, August 27, 2010 9:00:01 AM
> > > > Subject: RE: [R] About plot graphs
> > > >
> > > > There is a graphical parameter that controls whether a plot is
> square
> > > > or takes
> > > > up the maximum amount of room (rectangle), see ?par and look at
> the
> > > > entry for
> > > > pty.
> > > >
> > > >
> > > > It is possible that you set pty='s' or it may be that the plot
> method
> > > > sets it,
> > > > without us knowing what type of object Date and Test01$Date are
> we
> > > > don't know
> > > > which method is creating your plot and cannot be much more help
> (that
> > > > is meant
> > > > as a subtle hint to provide the information requested in the
> footer of
> > > > every
> > > > post and the posting guide).
> > > >
> > > > Some methods may set pty='s' as default but have an option to
> change
> > > > it.
> > > >
> > > > --
> > > > Gregory (Greg) L. Snow Ph.D.
> > > > Statistical Data Center
> > > > Intermountain Healthcare
> > > > greg.snow at imail.org
> > > > 801.408.8111
> > > >
> > > >
> > > > > -----Original Message-----
> > > > > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> > > > > project.org] On Behalf Of Stephen Liu
> > > > > Sent: Thursday, August 26, 2010 8:45 AM
> > > > > To: r-help at r-project.org
> > > > > Subject: [R] About plot graphs
> > > > >
> > > > > Hi folks,
> > > > >
> > > > > Following command prints 2 graphs side-by-side:-
> > > > > layout(matrix(1:2, nrow=1))
> > > > > plot(Date,Input_No.)
> > > > > plot(Test01$Date, Test01$Input_No.)
> > > > >
> > > > > However each is a square graph I need a rectangular layout.
> Pls
> > > > advise
> > > > > how to
> > > > > make it. TIA
> > > > >
> > > > > B.R.
> > > > > satimis
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ______________________________________________
> > > > > 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.
> > > >
> > > >
> > > >
> > > >
> > > > ______________________________________________
> > > > 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.
> > >
> > >
> > >
> > >
> > > ______________________________________________
> > > 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.
> >
>
> --
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> Dr. Gavin Simpson [t] +44 (0)20 7679 0522
> ECRC, UCL Geography, [f] +44 (0)20 7679 0565
> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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>
>
>
> ______________________________________________
> 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.
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