chime3D: Produce web graph of 3D graph that can be viewed using Chime...

In made4: Multivariate analysis of microarray data using ADE4

Description

chime3D 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 the chime plug-in.

Usage

chime3D(pdbfilename, classvec = NULL, title = NULL, filename = "output.html",
point.size=40,cols=NULL,  ...)

Arguments

pdbfilename	Input pdb filename, this is an output file from html3D.
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".
point.size	Numeric, size of the points in plot. Default is 40
cols	Vector, of colours to be used. The length of the vector must equal the length levels(classvec), that is the number of classes or groups of samples. The default is NULL, colours will be choosen using getcol.
...	further arguments passed to or from other methods

Details

Produces a html file, of a 3D graph which can be rotated using the FREEWARE chime (win, MacOS). Will colour samples by classvec if given one, and will produce chime script to highlight groups, spin on/off, and include button for restore for example see http://bioinf.ucd.ie/research/microarrays/.

Value

chime3D output is a html file that can be viewed in any web browser that supports the Chime plug-in.

Note

Note chime is only available on windows or Mac OS currently. Using the chime plug-in on Linux is slightly complicated but is available if the CrossOver Plug-in is installed. Instructions on installing this and chime on Linux are available at http://mirrors.rcsb.org/SMS/STINGm/help/chime_linux.html.

If you wish to view a 3D graph in Rasmol, you will need to execute a Rasmol script similar to

  load pdbfilename.pdb; 
  set axes on; 
  select off; 
  connect;
  set ambient 40; 
  rotate x 180; 
  select *;  
  spacefill 40
 

Author(s)

Aedin Culhane

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