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

Description Usage Arguments Details Value Note Author(s)

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

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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.