jmol3D: Produce web graph of 3D graph that can be viewed using Jmol...

In made4: Multivariate analysis of microarray data using ADE4

Description

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.

Usage

jmol3D(df, classvec=NULL, title=NULL, jmoldir="../jmol/Jmol.js",
         filename="output.html", point.size=40, xyz.axes =c(1:3), scaled=TRUE, ...)

Arguments

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.

Details

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.

Value

jmol3D output is a html file that can be viewed in any web browser that supports jmol http://jmol.sourceforge.net/.

Note

Note jmol must be downloaded on a local machine. Instructions on installing this are available at http://jmol.sourceforge.net/.

Author(s)

Aedin Culhane

made4 documentation built on Nov. 8, 2020, 6:49 p.m.