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Questions and answers > General discussions (Q&As)

How to make a nice visualization for angle distribution?

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whuang:
Recently I've read Dr. Lu's paper "The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex".

I found that Fig1.C

in the paper above is a very nice representation for plotting the histogram of angle. Dr. Lu, could share your experience with this plot with us? Thank you!

xiangjun:
Thanks for your interest in my GpU paper. I am glad that your find Fig 1C "a very nice representation for plotting the histogram of angle".

Per your request, here is the detailed step-by-step procedure I originally used to generate Fig 1C, up to the "raw" histogram of the phase angle of sugar ring pseudorotation.


* The data file named "key_pars_gu193.txt" is attached. It contains the phase angle of pseudorotation of the U and G sugar rings.

* The following R script is used to generate the "raw" figure (attached).
--- Code: ---library("circular")

pdat <- read.delim("key_pars_gu193.txt")
attach(pdat)

xfig(file="sugar_raw.fig", onefile=TRUE)
par(mfrow = c(1,2))
plot(circular(p1, units="degrees", rotation="clock"), zero=pi/2,
     stack=TRUE, bins=150, shrink=1.5)
plot(circular(p2, units="degrees", rotation="clock"), zero=pi/2,
     stack=TRUE, bins=150, shrink=1.5)
par(mfrow = c(1,1))
dev.off()

--- End code ---
Please note the followings:
* The R 'circular' package is used (http://cran.r-project.org/web/packages/ ... index.html)
* The xfig (http://www.xfig.org/) output device is used for later manually editing (not data points, but only cosmetic styles, of course) of the generated figure.  [attachment=1:1vq0n9no]key_pars_gu193.txt[/attachment:1vq0n9no]
[attachment=0:1vq0n9no]sugar_raw.png[/attachment:1vq0n9no]
HTH,

Xiang-Jun

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.