jmol3D {made4} | R Documentation |
jmol3D
produces a html web page with a 3D graph of a pdb file that can be rotated and manipulated in a web browser that
supports jmol.
jmol3D(df, classvec=NULL, title=NULL, jmoldir="../jmol/Jmol.js", filename="output.html", point.size=40, xyz.axes =c(1:3), scaled=TRUE, ...)
df |
A matrix or data.frame containing the x,y,z coordinates.
Typically the output from bga such as the $ls or $co files, or other xyz coordinates
($li or $co) produced by PCA, COA or other dudi . |
classvec |
Factor or vector which describes classes in the df. Default is NULL. If specified each group will be coloured in contrasting colours. |
title |
Character, the title (header) of the web page saved if writehtml is TRUE. The default is NULL . |
filename |
Character. The filename of the html to be saved. The default is output.html". |
xyz.axes |
Vector indicating which axes to use for x, y and z axes. By default, the first 3 columns of df. |
jmoldir |
Character indicating the local directory containing jmol. |
point.size |
Numeric, size of the points in plot. Default is 40. |
... |
Further arguments passed to or from other methods. |
Produces a html file, of a 3D graph which can be rotated using the opensource software jmol http://jmol.sourceforge.net/ which is a java based software that is open source. For example see http://bioinf.ucd.ie/people/aedin/jmoltest/test.html.
jmol3D output is a html file that can be viewed in any web browser that supports jmol http://jmol.sourceforge.net/.
Note jmol must be downloaded on a local machine. Instructions on installing this are available at http://jmol.sourceforge.net/.
Aedin Culhane