Explorer             package:aroma.core             R Documentation

_T_h_e _E_x_p_l_o_r_e_r _c_l_a_s_s

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

     Package:  aroma.core 
      *Class Explorer*

     'Object'
      '~~|'
      '~~+--'_'Explorer'_

     *Directly known subclasses:*
      ChromosomeExplorer

     public abstract static class *Explorer*
      extends Object

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

     Explorer(tags="*", ...)

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

    tags: A 'character' 'vector' of tags to be added to the output
          path.

     ...: Not used.

_F_i_e_l_d_s _a_n_d _M_e_t_h_o_d_s:

     *Methods:*

         'addIncludes'               -
         'display'                   Displays the explorer in the default browser.
         'getAlias'                  Gets the alias of the output set.
         'getAsteriskTags'           -
         'getFullName'               -
         'getName'                   Gets the name of the explorer.
         'getNames'                  Gets the names of the input samples.
         'getPath'                   -
         'getReportPathPattern'      -
         'getTags'                   Gets the tags of the explorer.
         'getTagsOfInput'            -
         'nbrOfArrays'               Gets the total number of arrays.
         'process'                   Generates image files, scripts and dynamic pages for the explorer.
         'setAlias'                  Sets the alias of the output set.
         'setArrays'                 Sets the arrays.
         'setReportPathPattern'      -
         'setSubname'                -
         'setup'                     -
         'splitByReportPathPattern'  -

     *Methods inherited from Object*:
      asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally,
     clearCache, clone, detach, equals, extend, finalize, gc,
     getEnvironment, getFields, getInstantiationTime,
     getStaticInstance, hasField, hashCode, ll, load, objectSize,
     print, registerFinalizer, save

_O_u_t_p_u_t _d_i_r_e_c_t_o_r_y _s_t_r_u_c_t_u_r_e:

     The _main directory_ of an Explorer report is
     'reports/<name>/<subname>/'. The '<name>' is typically the same as
     the name of the input data set, and the '<subname>' is typically
     the tags of ditto. This main directory is where main HTML document
     is stored.

     For each chip type, real or "virtual" (combined), there is a
     subdirectory with the same name as the chip type, i.e.
     'reports/<name>/<subname>/<chiptype>/'.

     For each chip type directory, there are set of subdirectories each
     specifying a so called _image layer_, e.g. an image layer showing
     the raw data, another containing the estimates of a model fit and
     so on.  Path format: 'reports/<name>/<subname>/<chiptype>/<image
     layer>/'. In this directory all image files are stored, e.g. PNG
     files.

     In some cases one do not want to all input tags to become part of
     the subname, but instead for instance use those to name the image
     layer(s). In such cases one has to override the default names.

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

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

