Exporting nice plots from R

深碍√TFBOYSˉ_ 2022-07-21 01:49 184阅读 0赞

A vital part of statistics is producing nice plots, an area where [R is outstanding][]. The graphical ablility of R is often listed as [a major reason][] for choosing the language. It is therefore funny that exporting these plots is such an issue in Windows. This post is all about how to export[anti-aliased][], [high resolution][] plots from R in Windows.

There are two main problems when exporting graphics from R:

*  Anti-aliasing is [not activated in Windows][] R (this does not apply to Linux or Mac).[Update][]: An important update is that the anti-aliasing is now included in R although not activated by default. [See section below.][Update]
 *  When increasing the resolution the labels automatically decrease and [become unreadable][]

My previous solution to this problem has been to export my graph to [a vector graphic][] (usually the SVG format), open it in [Inkscape][], and then export it to the resolution of choice. The vector graphic allows smooth scaling without me having to worry about the text becoming too small to read while at the same time adding the anti-aliasing. The down-side of this is that it is not really a convenient work-flow when you create [knitr/Sweave documents][knitr_Sweave documents] where many plots are simultaneously generated.

The post has several sections:

1.  [Raw export functions][]
2.  [The Cairo-package][]
3.  [The cairoDevice-package][]
4.  [Raw export functions with the type=”cairo” activated][Update]
5.  [Fills and anti-aliasing][]

## exporting ##

Let us start by looking at an exported plot from RStudio, clearly not something I would like to send to a journal:

[![A PNG Export from RStudio. Note the ragged looking line and the sharp letters.][]][A PNG Export from RStudio. Note the ragged looking line and the sharp letters.]A PNG EXPORT FROM RSTUDIO. NOTE THE RAGGED LOOKING LINE AND THE SHARP LETTERS.

So the first alternative would be the standard library. We can kick-off with the svg() function as I mentioned it earlier (**Note**: If you can’t see the plot then your browser is probably old and does not support svg images):

[?][Link 1]   RSPLUS

[![A scalable vector image of the plot by the standard svg() function. The plot has long labels to enhance size comparison between different plots.][A scalable vector image of the plot by the standard svg_ function. The plot has long labels to enhance size comparison between different plots.]][A scalable vector image of the plot by the standard svg_ function. The plot has long labels to enhance size comparison between different plots.]

All images in this post use the same basic settings with minor tweaks:

*  Width = 5 inches
 *  Height = 4 inches
 *  pointsize = 12

If we now do the same using the png() command we also have to set the resolution. I’m using[72 dpi (pixels/inch)][72 dpi _pixels_inch], as 1 point by the modern definition is 1/72 of the international inch and therefore a good start instead of the 96 dpi that Windows uses. As you can see the size of the labels are very similar to the svg():

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none"><a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">png</a>(filename="Std_PNG.png", 
 <a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/units.html" style="color:rgb(116,51,153)" rel="nofollow">units</a>="in", 
 width=5, 
 height=4, 
 pointsize=12, 
 res=72)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![A PNG image based on the png() command.][A PNG image based on the png_ command.]][A PNG image based on the png_ command.]A PNG IMAGE BASED ON THE PNG() COMMAND. IT IS CLEARLY NOT AS SMOOTH AS WE WOULD WANT IT TO BE…

**Note:** The Cairo packages are obsolete as it usually is built in nowadays, all you need to do is remember to reference it – see my [update][Update]

## the cairo-package ##

The Cario package is an excellent choice for getting antia-aliased plots in Windows. Here’s the same plot from the Cairo package (the background is now transparent):

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none"><a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/library.html" style="color:rgb(116,51,153)" rel="nofollow">library</a>(Cairo)
Cairo(<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/file.html" style="color:rgb(116,51,153)" rel="nofollow">file</a>="Cairo_PNG_72_dpi.png", 
 type="png",
 <a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/units.html" style="color:rgb(116,51,153)" rel="nofollow">units</a>="in", 
 width=5, 
 height=4, 
 pointsize=12, 
 dpi=72)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![The same plot using the Cairo package, note the much smoother line and text][The same plot using the Cairo package_ note the much smoother line and text]][The same plot using the Cairo package_ note the much smoother line and text]THE SAME PLOT USING THE CAIRO PACKAGE, NOTE THE MUCH SMOOTHER LINE AND TEXT

If we want to increase the resolution of the plot we can’t just change the resolution parameter:

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">Cairo(<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/file.html" style="color:rgb(116,51,153)" rel="nofollow">file</a>="Cairo_PNG_96_dpi.png", 
 type="png",
 <a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/units.html" style="color:rgb(116,51,153)" rel="nofollow">units</a>="in", 
 width=5, 
 height=4, 
 pointsize=12, 
 dpi=96)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![A 96 dpi version of the same image][]][A 96 dpi version of the same image]A 96 DPI VERSION OF THE SAME IMAGE

We also have to change the point size, the formula is size \* new resolution DPI / 72 DPI:

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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9</pre> </td> 
 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">Cairo(<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/file.html" style="color:rgb(116,51,153)" rel="nofollow">file</a>="Cairo_PNG_96_dpi_adj.png", 
 type="png",
 <a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/units.html" style="color:rgb(116,51,153)" rel="nofollow">units</a>="in", 
 width=5, 
 height=4, 
 pointsize=12*92/72, 
 dpi=96)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![Adjusted point size results in the labels remaining the proper size][]][Adjusted point size results in the labels remaining the proper size]ADJUSTED POINT SIZE RESULTS IN THE LABELS REMAINING THE PROPER SIZE

If we double the image size we also need to double the point size:

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">Cairo(<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/file.html" style="color:rgb(116,51,153)" rel="nofollow">file</a>="Cairo_PNG_72_dpi_x_2.png", 
 type="png",
 <a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/units.html" style="color:rgb(116,51,153)" rel="nofollow">units</a>="in", 
 width=5*2, 
 height=4*2, 
 pointsize=12*2, 
 dpi=72)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![Double size image][]][Double size image]DOUBLE SIZE IMAGE

## the cairodevice package ##

An alternative to the Cairo package is the cairoDevice package. It uses the same engine but has a slightly different syntax and due to it’s limitation in setting the resolution it really doesn’t work that well. Lets try the same as above:

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none"># Detach the Cairo package just to make
# sure that there aren't any conflicts
<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/detach.html" style="color:rgb(116,51,153)" rel="nofollow">detach</a>("package:Cairo")
<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/library.html" style="color:rgb(116,51,153)" rel="nofollow">library</a>(cairoDevice)
Cairo(filename="cairoDevice_SVG_pt12.svg", 
 surface="png", 
 width=5, 
 height=4, 
 pointsize=12)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![A completely differently looking image - not even remotely close to the original][]][A completely differently looking image - not even remotely close to the original]A COMPLETELY DIFFERENTLY LOOKING IMAGE – NOT EVEN REMOTELY CLOSE TO THE ORIGINAL

To be fair the default point size of the cairoDevice package, 8 points is less than for the Cairo package but even with that setting the image looks not that great:

[![Using the default 8 points still looks funny][]][Using the default 8 points still looks funny]USING THE DEFAULT 8 POINTS STILL LOOKS FUNNY

After some tweaking I found that 5.2 points was fairly similar:

[![A tweaked cairoDevice plot - looks OK but the font is a big disappointment][]][A tweaked cairoDevice plot - looks OK but the font is a big disappointment]A TWEAKED CAIRODEVICE PLOT – LOOKS OK BUT THE FONT IS A BIG DISAPPOINTMENT

## summary ##

The Cairo package does the job nicely and without too much hassle you can get the look exactly right. If you want the background to be white just add the *bg* parameter:

[?][Link 1]   RSPLUS

<table style="border-collapse:collapse; border-spacing:0px; border:1px solid rgb(231,231,231); width:656px; margin:0px -1px 24px 0px"> 
 <tbody> 
 <tr> 
 <td style="vertical-align:top; padding:6px 24px; text-align:right; color:rgb(102,102,102); overflow:visible; border-right-width:1px; border-right-style:solid; border-right-color:rgb(176,190,199); table-layout:auto; width:10px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231); background-color:rgb(221,238,255)"> <pre style="font-family:Monaco,Consolas,'Andale Mono','DejaVu Sans Mono',monospace; line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">1
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 <td style="vertical-align:top; padding:6px 24px; border-top-width:1px; border-top-style:solid; border-top-color:rgb(231,231,231)"> <pre style="line-height:1.333; padding:0px; border:none; margin-top:0px; margin-bottom:24px; width:auto; float:none; clear:none; overflow:visible; background:none">Cairo(<a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/file.html" style="color:rgb(116,51,153)" rel="nofollow">file</a>="Cairo_PNG_72_dpi_white.png", 
 bg="white",
 type="png",
 <a href="http://astrostatistics.psu.edu/su07/R/html/graphics/html/units.html" style="color:rgb(116,51,153)" rel="nofollow">units</a>="in", 
 width=5, 
 height=4, 
 pointsize=12, 
 dpi=72)
my_sc_plot(data)
<a href="http://astrostatistics.psu.edu/su07/R/html/stats/html/summary.lm.html" style="color:rgb(116,51,153)" rel="nofollow">dev.off</a>()</pre> </td> 
 </tr> 
 </tbody> 
</table>

[![The same as above but with a white background][]][The same as above but with a white background]THE SAME AS ABOVE CAIRO IMAGES BUT WITH A WHITE BACKGROUND

# Update #

After Matt Neilsons excellent comment I’ve discovered that the standard export functions actually allow for anti-aliasing with built-in cairo support. Another excellent part is that the dpi now works exactly as expected – you don’t need to adjust the point size

[R is outstanding]: http://cran.r-project.org/web/views/Graphics.html
[a major reason]: http://monkeysuncle.stanford.edu/?p=367
[anti-aliased]: http://www.pantherproducts.co.uk/index.php?pageid=antialiasing
[high resolution]: http://www.prepressure.com/design/basics/resolution
[not activated in Windows]: http://stackoverflow.com/questions/6023179/anti-aliasing-in-r-graphics-under-windows-as-per-mac
[Update]: http://gforge.se/2013/02/exporting-nice-plots-in-r/#update
[become unreadable]: http://civilstat.com/?p=557
[a vector graphic]: http://en.wikipedia.org/wiki/Vector_graphics
[Inkscape]: http://inkscape.org/
[knitr_Sweave documents]: http://gforge.se/2012/08/getting-started-with-knitr-and-sweave/
[Raw export functions]: http://gforge.se/2013/02/exporting-nice-plots-in-r/#Raw_export
[The Cairo-package]: http://gforge.se/2013/02/exporting-nice-plots-in-r/#Cairo
[The cairoDevice-package]: http://gforge.se/2013/02/exporting-nice-plots-in-r/#cairoDevice
[Fills and anti-aliasing]: http://gforge.se/2013/02/exporting-nice-plots-in-r/#fills
[A PNG Export from RStudio. Note the ragged looking line and the sharp letters.]: /images/20220720/0d535671a2de4deea6e14eaa6ccfdb93.png
[Link 1]: http://www.ericbess.com/ericblog/2008/03/03/wp-codebox/#examples
[A scalable vector image of the plot by the standard svg_ function. The plot has long labels to enhance size comparison between different plots.]: /images/20220720/3fa786a5a50c4b07bbca677518a6c1c0.png
[72 dpi _pixels_inch]: http://en.wikipedia.org/wiki/Dots_per_inch
[A PNG image based on the png_ command.]: /images/20220720/f1d148bb2c1849c3a4a268d751e9a205.png
[The same plot using the Cairo package_ note the much smoother line and text]: /images/20220720/5f3cc297980b4573a8a040519a5f9cc9.png
[A 96 dpi version of the same image]: /images/20220720/9186fc467911417da6c38755770ec3d8.png
[Adjusted point size results in the labels remaining the proper size]: /images/20220720/0a9a0679f8254e24a50adf4d737233c7.png
[Double size image]: /images/20220720/06577936a2e547c792c15d6ff3f6d6c6.png
[A completely differently looking image - not even remotely close to the original]: /images/20220720/f80cee8a754b40ecbf126fc72f647a24.png
[Using the default 8 points still looks funny]: /images/20220720/acbef5990a3a4c59a832cd4ae5377d67.png
[A tweaked cairoDevice plot - looks OK but the font is a big disappointment]: /images/20220720/dc760bb4251b4d63b7c42b6f4cc7773a.png
[The same as above but with a white background]: /images/20220720/ae2269f11823425a93f9f0beae82d795.png