### Author Topic: How to make a nice visualization for angle distribution?  (Read 5293 times)

#### whuang

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##### How to make a nice visualization for angle distribution?
« on: October 12, 2010, 11:22:56 am »
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!
« Last Edit: November 16, 2019, 12:20:54 am by xiangjun »

#### xiangjun

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##### Re: How to make a nice visualization for angle distribution?
« Reply #1 on: October 12, 2010, 11:30:56 pm »
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: [Select]
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()
Please note the followings:
[attachment=1:1vq0n9no]key_pars_gu193.txt[/attachment:1vq0n9no]
[attachment=0:1vq0n9no]sugar_raw.png[/attachment:1vq0n9no]
HTH,

Xiang-Jun
Dr. Xiang-Jun Lu ［律祥俊］
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.