jmol3D {made4} | R Documentation

## Produce web graph of 3D graph that can be viewed using Jmol in web browser

### 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

[Package made4 version 1.64.0 Index]