ChromosomeExplorer        package:aroma.core        R Documentation

_T_h_e _C_h_r_o_m_o_s_o_m_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 ChromosomeExplorer*

     'Object'
      '~~|'
      '~~+--''Explorer'
      '~~~~~~~|'
      '~~~~~~~+--''ChromosomeExplorer'

     *Directly known subclasses:*


     public static class *ChromosomeExplorer*
      extends _Explorer_

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

     ChromosomeExplorer(model=NULL, zooms=2^(0:7), ..., version=c("3"))

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

   model: A 'CopyNumberChromosomalModel' object.

   zooms: An positive 'integer' 'vector' specifying for which zoom
          levels the graphics should be generated.

     ...: Not used.

 version: The version of the Explorer HTML/Javascript generated/used.

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

     *Methods:*

         'display'          -
         'getChromosomes'   Gets the chromosomes available.
         'getFullNames'     -
         'getModel'         Gets the model.
         'getNames'         -
         'getPath'          -
         'getSampleLabels'  -
         'getZooms'         -
         'indexOf'          -
         'process'          Generates image files, scripts and dynamic pages for the explorer.
         'setArrays'        Sets the arrays.
         'setCytoband'      -
         'setZooms'         -

     *Methods inherited from Explorer*:
      addIncludes, addIndexFile, display, getAlias, getArraysOfInput,
     getAsteriskTags, getFullName, getIncludePath, getMainPath,
     getName, getNameOfInput, getNames, getParallelSafe, getPath,
     getReportPathPattern, getSampleLayerPrefix, getSubname, getTags,
     getTagsOfInput, getTemplatePath, nbrOfArrays, process, setAlias,
     setArrays, setParallelSafe, 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

_G_e_n_e_r_a_t_i_n_g _P_N_G _i_m_a_g_e_s:

     In order to get better looking graphs, but also to be able to
     generate bitmap images on systems without direct bitmap support,
     which is the case when running R in batch mode or on Unix without
     X11 support, images are created using the 'png2' device (a wrapper
     for 'bitmap()' immitating 'png()').  The 'png()' is only used if
     'png2()', which requires Ghostscript, does not. Note, when images
     are created using 'png2()', the images does not appear
     immediately, although the function call is completed, so be
     patient.

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

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

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

     'CopyNumberChromosomalModel'.

