jmol3D                 package:made4                 R Documentation

_P_r_o_d_u_c_e _w_e_b _g_r_a_p_h _o_f _3_D _g_r_a_p_h _t_h_a_t _c_a_n _b_e _v_i_e_w_e_d _u_s_i_n_g _J_m_o_l _i_n _w_e_b _b_r_o_w_s_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     '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.

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

      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.

_D_e_t_a_i_l_s:

     Produces a html file, of a 3D graph which can be rotated using the
     opensource software jmol <URL: http://jmol.sourceforge.net/> which
     is a java based software that is open source.    For example see
     <URL: http://bioinf.ucd.ie/people/aedin/jmoltest/test.html>.

_V_a_l_u_e:

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

_N_o_t_e:

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

_A_u_t_h_o_r(_s):

     Aedin Culhane

