pmAbst2HTML             package:annotate             R Documentation

_H_T_M_L _G_e_n_e_r_a_t_i_o_n _f_o_r _P_u_b_M_e_d _A_b_s_t_r_a_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function will take a 'pubMedAbst' object, or a list of these
     objects and generate a web page that will list the titles of the
     abstracts and link to their full page on PubMed

_U_s_a_g_e:

     pmAbst2HTML(absts, filename, title, frames = FALSE, table.center = TRUE)

_A_r_g_u_m_e_n_t_s:

   absts: A list of 'pubMedAbst' (or a single object)

filename: The output filename.  If 'frames' is 'FALSE', this is the
          name of the single output file and defaults to 'absts.html'. 
          Otherwise, this is taken to be the base of a set of
          filenames, and the default base is the empty string.  See
          'value' for more information on output files.

   title: Extra title information for your listing

  frames: If 'frames' is 'TRUE', the resulting page will use HTML
          frames, resulting in a more complex set of output pages.

table.center: If TRUE, will center the listing of abstracts

_D_e_t_a_i_l_s:

     This function uses the 'Entrez' functionality provided by NCBI to
     retrieve the abstract URL at the PubMed site.  It will then create
     a tabular webpage which will list the titles of the abstracts
     provided and have them link to the appropriate PubMed page.  If
     'frames' is 'TRUE', the table of links will be on the left hand
     side of the page and the right hand will link directly to the
     appropriate PubMed page.

_V_a_l_u_e:

     If 'frames' is 'FALSE', a simple HTML file is created with the
     name specified by 'filename'.

     If 'frames' is 'TRUE', then there are four HTML files created, of
     the form 'XXXtop.html', 'XXXside.html', 'XXXmain.html' and
     'XXXindex.html', where 'XXX' is the string provided by 'filename'.

_N_o_t_e:

     This function is part of the Bioconductor project at the
     Dana-Farber Cancer Institute to provide Bioinformatics
     functionalities through R

_A_u_t_h_o_r(_s):

     Jeff Gentry

_S_e_e _A_l_s_o:

     'pubMedAbst'

_E_x_a_m_p_l_e_s:

             x <- pubmed("9695952","8325638","8422497")
             a <- xmlRoot(x)
             numAbst <- length(xmlChildren(a))
             absts <- list()
             for (i in 1:numAbst) {
                absts[[i]] <- buildPubMedAbst(a[[i]])
             }
             ## First try it w/o frames - using a temporary
             ## file for the output
             fname <- tempfile()
             pmAbst2HTML(absts,filename=fname)

             if (interactive())
               browseURL(paste("file://",fname,sep=""))

             ## Now try it w/ frames, using temporary files again.
             fnameBase <- tempfile()
             pmAbst2HTML(absts,filename=fnameBase, frames=TRUE)

             if (interactive())
               browseURL(paste("file://",fnameBase,"index.html",sep=""))

