Basic: setting resolution and size of an R graphic
If you specifically need the plot to have a dimension measured in
pixels, then you need to use a bitmapped format such as png and specify
the output to be the size you require:
png("test.png", width = 300, height = 300, ...)
DoYourPlotHere()
dev.off()
Do this directly using the png() device, rather than trying to convert
the image format, which almost always introduces "noise".
Since you are using a bitmapped format, you will experience the tradeoff
with respect to the image quality (ie. pixelated) as compared to a
vector based format such as PDF or PS.
I would re-verify the requirements for the journal to which you are
submitting the article relative to what they need for image specs. It
seems unusual for a journal to request an image in this fashion, unless
it is a photograph where a jpg format may be preferred or perhaps for
online publication on a web page.
HTH,
Marc Schwartz
On Tue, 2005-10-25 at 08:57 +0200, Dr. med. Peter Robinson wrote:
Thanks Marc and Jim for the tips. The PDF file that I create with R looks about the same as the one you created. However, I need to get the graphic to be a certain size (300 pixels wide). I have been using the ImageMagick program to do so for other graphics: convert test.pdf -resize 300x300 out.pdf then out.pdf looks rather poor (pixelly). The original image is too big. ANy ideas? Thanks a lot,Peter Am Mo, 24.10.2005, 22:53, schrieb Marc Schwartz (via MN):
On Mon, 2005-10-24 at 22:32 +0200, Dr. med. Peter Robinson wrote:
Dear List, I am sorry if this perhaps a too basic question, but I have not found an answer in Google or in the R help system. I am trying to use R to do a very simple analysis of some data (RT-PCR and Western analysis) with a T-test and to plot the results as a histogram with error bars. (I have pasted an example script at the bottom of this mail). In order to use this for publication, I would like to adjust the resolution and size of the final image. However, even using file types such as postscript or pdf that are vector based, I get rather bad-looking results with
pdf(file="test.pdf") source("script at bottom of mail") dev.off()
using either pdf or postscript or jpg devices. Therefore I would like to ask the list, how to best produce a graphic from the script below that would fit into one column of a published article and have a high resolution (as eps, or failing that tiff or png)? Thanks in advance for any advice, Peter
<Snip of code>
What OS are you on?
Running your example on FC4, I get the attached output for a pdf().
I suspect that on your OS, the height and width arguments are not
appropriate by default.
Thus, you may need to adjust your pdf (or postscript) function call to
explicitly specify larger height and width arguments.
Also note that to generate an EPS file, pay attention to the details
section of ?postscript, taking note of the 'onefile', 'horizontal' and
'paper' arguments and settings.
Also, check with your journal to see if they specify dimensions for such
graphics so that you can abide by their specs if provided. If they are
using LaTeX, there are means of specifying and/or adjusting the height
and/or width specs in the code based upon proportions of various measures
(ie. \includegraphics[width=0.9\textwidth]{GraphicsFile.eps} ).
HTH,
Marc Schwartz