[R] Yet another plotting hint - choosing the proper device to produce plots for Word

Jason Rupert jasonkrupert at yahoo.com
Thu Aug 13 17:29:30 CEST 2009 

Magically, the eps version seems to fix the "not coloring in the lines" issue observed when using the WMF device - note that the issue was observed when viewing it on the screen and after printing it out.  

However, with eps, the color of the points when using pch 21 appears to stay within the boundary of the circle when viewed on the screen and when printed.  


Now, regarding the addition of a TIFF preview, I tried to uses GSView to add a preview via the following instructions:
http://pages.cs.wisc.edu/~ghost/gsview/gsviewen.htm#EPS_Preview
Unfortunately the "Add EPS Preview" option is greyed out for eps file generated with the following code shown below.

Do you have any further suggestions, about what I should try to produce a reasonable preview for the eps? 

Thank you again for any feedback and insights. 

postscript(file= as.character("TestFigure.eps"), height = 6, width = 7, pointsize = 10, paper = "special", onefile = FALSE, horizontal=F)
plot(-4:4, -4:4, type = "n")# setting up coord. system
points(rnorm(200), rnorm(200), col = "red", pch=20)
points(rnorm(100)/2, rnorm(100)/2, col = "blue", cex = 1.5, pch=20)
dev.off()


--- On Thu, 8/13/09, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:

> From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
> Subject: Re: [R] Yet another plotting hint - choosing the proper device to produce plots for Word
> To: "Jason Rupert" <jasonkrupert at yahoo.com>
> Cc: "Scott Sherrill-Mix" <shescott at mail.med.upenn.edu>, r-help at r-project.org
> Date: Thursday, August 13, 2009, 7:34 AM
> 
> On Thu, 2009-08-13 at 04:53 -0700, Jason Rupert wrote:
> > Scott, 
> > 
> > Thanks for your response and insight. 
> > 
> > I call what I'm seeing - "Not coloring within the
> lines" :)
> > 
> > When using pch 19, 20, or 21, it looks like the fill
> does no stay
> > within the perimeter of the circle or properly fill
> the circle, i.e.
> > some blank area left.  It is demonstrated at the
> following Nabble post
> > location:    
> > 
> > http://n2.nabble.com/Unusual-Plotting-Artifacts-td3437365.html
> > 
> > I guess I would like to use a device that does not
> have this issue and
> > also provides image that look well electronically in
> Word and also
> > print well.  They need to look good when
> importing because most of the
> > reviews will be conducted electronically in Word, and
> it needs to look
> > good when printed because one or two folks will review
> a hard copy.
> 
> I wouldn't be so quick to blame the device itself - the
> rendered could
> also be having difficulties with metafiles, even MS own
> software has
> problems.
> 
> >   
> > 
> > You mentioned that EPS has a weakness because Word
> shows a low
> > resolution version.  Is there another device that
> gets around this
> > problem?  At this point filesize is not an
> issue.
> 
> You could add the preview yourself using ghostscript and
> gsview on
> Windows - IIRC you get a few options as to how the preview
> should be
> generated. It is still going to be low-res though, compared
> to the
> printed version.
> 
> Ultimately, vector based images are going to render better
> when printed
> throughout this process, so think about the ultimate
> delivery of this
> document and ease of conversion to things like PDF if that
> is on the
> cards. Bitmap images (PNG etc) might look good on screen
> but print
> poorly or loose resolution if manipulated etc.
> 
> Depends on the work flow you have in mind, but perhaps a
> high res PNG or
> TIFF might be better if file size is irrelevant if you have
> to use Word
> and have to review on screen.
> 
> G
> 
> >   
> > 
> > Thank you again for all your help and feedback. 
>   
> > 
> > 
> > 
> > 
> > 
> > --- On Thu, 8/13/09, Gavin Simpson <gavin.simpson at ucl.ac.uk>
> wrote:
> > 
> > > From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
> > > Subject: Re: [R] Another Plotting Hint - changing
> fill color for points
> > > To: "Scott Sherrill-Mix" <shescott at mail.med.upenn.edu>
> > > Cc: "Jason Rupert" <jasonkrupert at yahoo.com>,
> r-help at r-project.org
> > > Date: Thursday, August 13, 2009, 3:41 AM
> > > On Wed, 2009-08-12 at 23:36 -0400,
> > > Scott Sherrill-Mix wrote:
> > > > I don't really use Word or .wmf but maybe
> try a high
> > > pixel count .png e.g.
> > > >
> png('test.png',height=480*5,width=480*5,res=72*5)
> > > > plot(1:10, col = "red", bg = "grey", pch=21,
> cex
> > > =1.7)
> > > > dev.off()
> > > > 
> > > > 
> > > > Scott
> > > 
> > > An EPS is likely to give better resolution if the
> document
> > > is intended
> > > to be printed. An EPS image will likely also have
> a much
> > > smaller file
> > > size, if that is important.
> > > 
> > > One problem with EPS files in Word is that, at
> least in the
> > > versions I
> > > have used (up to Office 11), Word displays a low
> resolution
> > > preview of
> > > the image on screen, so it doesn't look quite so
> good on
> > > screen, but
> > > printing is fine.
> > > 
> > > Jason, did you print your document containing the
> wmf? What
> > > you might be
> > > seeing could just be the effects of antialiasing
> or some
> > > other
> > > processing going on to display the image in Word
> on screen
> > > and not be
> > > present in the printed version.
> > > 
> > > To get an eps, use postscript() with 'paper' and
> 'onefile'
> > > set
> > > appropriately
> > > 
> > > eps('test.eps' height = 6, width = 7, pointsize =
> 10,
> > >     paper = "special",
> onefile = FALSE)
> > > ## plotting
> > > dev.off()
> > > 
> > > HTH
> > > 
> > > G
> > > 
> > > > 
> > > > Scott Sherrill-Mix
> > > > Department of Microbiology
> > > > University of Pennsylvania
> > > > 402B Johnson Pavilion
> > > > 3610 Hamilton Walk
> > > > Philadelphia, PA  19104-6076
> > > > 
> > > > 
> > > > 
> > > > On Wed, Aug 12, 2009 at 6:17 PM, Jason
> Rupert<jasonkrupert at yahoo.com>
> > > wrote:
> > > > > This worked great.
> > > > >
> > > > >
> > > > > Regarding the second question - can you
> expound a
> > > bit more on the effect of the device?  Right
> now, as
> > > shown by the test code because I am on a Windows
> machine and
> > > need to import the image to Word I am using
> WMF.  Is
> > > there a better device that I should use that will
> help with
> > > the presolution of the points that are
> drawn?  For
> > > example, I can see white pixesl on the blue
> circles, and
> > > notice that is not a perfect circle.  Thanks
> for any
> > > information about a better way to go:
> > > > >
> > > > >
> > >
> win.metafile(file=as.character(figure_file_name_and_path),
> > > pointsize = 10)
> > > > > plot(-4:4, -4:4, type = "n")# setting
> up coord.
> > > system
> > > > > points(vals_201, vals_200, col = "red",
> bg =
> > > "grey", pch=21, cex =1..7)
> > > > > #points(vals_201, vals_200, col =
> "grey", bg =
> > > "white", pch=21, cex =1.5)
> > > > > points(rnorm(100)/2, rnorm(100)/2, col
> = "blue",
> > > bg = "blue",  pch=21, cex =1.5)
> > > > > dev.off()
> > > > >
> > > > >
> > > > > Thanks again.
> > > > >
> > > > > --- On Wed, 8/12/09, Sarah Goslee
> <sarah.goslee at gmail.com>
> > > wrote:
> > > > >
> > > > >> From: Sarah Goslee <sarah.goslee at gmail.com>
> > > > >> Subject: Re: [R] Another Plotting
> Hint -
> > > changing fill color for points
> > > > >> To: "Jason Rupert" <jasonkrupert at yahoo.com>,
> > > "r-help" <r-help at r-project.org>
> > > > >> Date: Wednesday, August 12, 2009,
> 4:56 PM
> > > > >> Yes, you can do that. You need to
> > > > >> specify pch in the range of 21-25,
> > > > >> and can then
> > > > >> specify both col and bg (background
> color).
> > > Oddly, the help
> > > > >> for this option is
> > > > >> under ?points rather than ?par or
> ?pch, but
> > > there are many
> > > > >> examples.
> > > > >>
> > > > >> Your second question would depend
> heavily on
> > > the device you
> > > > >> use and its
> > > > >> associated settings, but using the
> above
> > > solution should
> > > > >> solve your problem.
> > > > >>
> > > > >> Sarah
> > > > >>
> > > > >> On Wed, Aug 12, 2009 at 5:29 PM,
> Jason
> > > Rupert<jasonkrupert at yahoo.com>
> > > > >> wrote:
> > > > >> >
> > > > >> > Is it possible to change the
> fill color
> > > of a point?
> > > > >>  For example, the outer color
> being
> > > "Blue" and inner color
> > > > >> being "Grey".
> > > > >> > I've tried changing "col" and
> "bg", but
> > > that does not
> > > > >> seem to have the desired effect.
> > > > >> >
> > > > >> > Below is another attempt, but
> the pixel
> > > resolution of
> > > > >> the points function does not appear
> to be
> > > high enough for
> > > > >> this to work:
> > > > >> >
> > > > >> >
> > > figure_file_name_and_path<-paste("Test.wmf",
> > > > >> sep="")
> > > > >> >
> > > > >> > vals_200<-rnorm(200)
> > > > >> > vals_201<-rnorm(200)
> > > > >> >
> > > > >> >
> > > > >>
> > >
> win.metafile(file=as.character(figure_file_name_and_path),
> > > > >> pointsize = 10)
> > > > >> > plot(-4:4, -4:4, type = "n")#
> setting up
> > > coord.
> > > > >> system
> > > > >> > points(vals_201, vals_200, col
> = "blue",
> > > bg = "white",
> > > > >> pch=19, cex =1.7)
> > > > >> > points(vals_201, vals_200, col
> = "grey",
> > > bg = "white",
> > > > >> pch=19, cex =1.5)
> > > > >> > points(rnorm(100)/2,
> rnorm(100)/2, col =
> > > "blue", bg =
> > > > >> "white",  pch=19, cex =1.5)
> > > > >> > dev.off()
> > > > >> >
> > > > >> > As a second question, is there
> any way
> > > to increase the
> > > > >> pixel resolution of the points
> produced on
> > > the plot so that
> > > > >> they are perfect circles.  I
> just
> > > noticed that the fill
> > > > >> does not perfectly fill the points
> on the
> > > plot and there are
> > > > >> some pixels outside the circle.
> > > > >> >
> > > > >> > Thanks again.
> > > > >> >
> > > > >>
> > > > >>
> > > > >> --
> > > > >> Sarah Goslee
> > > > >> http://www.functionaldiversity.org
> > > > >>
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> ______________________________________________
> > > > > 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.
> > > -- 
> > >
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> > >  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
> > >
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > ______________________________________________
> > 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. 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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