aln2html                package:bio3d                R Documentation

_C_r_e_a_t_e _a _H_T_M_L _P_a_g_e _F_o_r _a _G_i_v_e_n _A_l_i_g_n_m_e_n_t

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

     Renders a sequence alignment as coloured HTML suitable for viewing
     with a web browser.

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

     aln2html(aln, file="alignment.html", Entropy=0.5, append=TRUE,
              caption.css="color: gray; font-size: 9pt",
              caption="Produced by <a href=\"http://mccammon.ucsd.edu/~bgrant/bio3d/\">Bio3D<a>",
              fontsize="11pt", bgcolor=TRUE, colorscheme="clustal")

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

     aln: an alignment list object with 'id' and 'ali' components,
          similar to that generated by 'read.fasta'. 

    file: name of output html file.  

 Entropy: conservation 'cuttoff' value below which alignment columns
          are not coloured. 

  append: logical, if TRUE output will be appended to 'file';
          otherwise, it will overwrite the contents of 'file'. 

caption.css: a character string of css options for rendering 'caption'
          text. 

 caption: a character string of text to act as a caption. 

fontsize: the font size for alignment characters. 

 bgcolor: background colour. 

colorscheme: conservation colouring scheme, currently only "clustal" is
          supported with alternative arguments resulting in an entropy
          shaded alignment.

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

     Called for its effect.

_N_o_t_e:

     Your web browser should support style sheets.

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

     Barry Grant

_R_e_f_e_r_e_n_c_e_s:

     Grant, B.J. et al. (2006) _Bioinformatics_ *22*, 2695-2696.

_S_e_e _A_l_s_o:

     'read.fasta', 'write.fasta', 'seqaln'

_E_x_a_m_p_l_e_s:

     ## Read an example alignment
     aln <- read.fasta(system.file("examples/kinesin_xray.fa",package="bio3d"))

     ## Produce a HTML file for this alignment
     aln2html(aln, append=FALSE, file="eg.html")
     aln2html(aln, colorscheme="ent", file="eg.html")
     ## View/open the file "eg.html" in your web browser

