markup            package:BiocCaseStudies            R Documentation

_M_a_r_k_u_p _c_o_m_m_a_n_d_s.

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

     Usage of predefined markup commands for layout of Bioc Case
     Studies book.

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

     The following markup commands, LaTeX makros and environments are
     available for controling the layout and structure of the book:


   '_E_x': environment for exercise chunks.

   '_s_o_l_u_t_i_o_n': environment for solutions to the exercises.

   '_m_y_i_n_c_f_i_g': macro for figure environments with three parameters: (1)
        figure filename (2) figure width (3) figure caption

   '_s_o_l_f_i_g': macro for figure environments within solution chunks. This
        is necessary because LaTex doesn't allow for floats within
        minipage environments.

   '_m_y_r_e_f': reference to other labs/chapters. For the book this is a
        simplewrapper around ref ignoring the second argument, for the
        labs this command is replaced in the useRlabs.sty file allowing
        for referencing bbetween the individual documents.

   '_b_o_o_k_l_a_b': macro for conditional text input with two parameters. The
        first parameter will be used for the book while the second will
        be used for the labs.

     The following makros will automatically create index entries as
     side effect. Apart from that they do text highlighting as well.

   '_R': the R language glyph (in sans serif font)

   '_R_p_a_c_k_a_g_e': an R package (in bold font)

   '_R_c_l_a_s_s': an R class (in italics)

   '_R_m_e_t_h_o_d': an R method (in small typewriter font)

   '_R_f_u_n_c_t_i_o_n': an R function (in small typewriter font)

     Implicit index terms can be generated using


   '_i_n_d_e_x_T_e_r_m': with the optional first argument giving the actual term
        and the second argument giving a string that appears in the
        text. E.g. 'indexTerm[tree]{trees}' would give you "trees" in
        the text but create an index for "tree". Omitting the optional
        first argument will create an index for the same string that
        appears in the text.

     Some more usful text markup that doesn't create indices:

   '_R_o_b_j_e_c_t': an R object (in small typewriter font)

   '_R_f_u_n_a_r_g': the agument to an R function (in italics)

   '_c_o_d_e': typewriter font

   '_t_e_r_m': whatever '\{emph}' is set to

   '_f_i_l_e': italics

   '_r_e_g': The registered trademark glyph

     The following environments are used to structure the document and
     for parsing . They do not impose any layout.


   '_c_h_a_p_t_e_r_h_e_a_d_e_r': this contains title, authors and abstract of the
        chapter/lab

   '_c_h_a_p_t_e_r_b_o_d_y:' this contains the actual chapter body

   '_c_h_a_p_t_e_r_t_r_a_i_l_e_r:' this contains session info and references for a
        chapter

   '_y_a_a': This is a wrapper for 'input' also setting the graphics
        include path. Its first parameter is filename, second parameter
        is graphics path

     Color and options


   _c_o_l_o_r_s: There are some predefined colors that should be used
        consistantly throughout the whole book for things like
        histograms, barplots, etc. They are defined by
        'BiocCaseStudies' as objects 'lcol1', 'lcol2' and 'lcol3' for
        light colors, and 'dcol1', 'dcol2' and 'dcol3' for dark colors.

   _S_w_e_a_v_e _o_p_t_i_o_n_s: The boolean option 'hideme' can be used in Sweave
        code chunks that should not be part of the Stangle output. This
        only effects Stangle, so a "regular" Sweave will evaluate these
        chunks. The intention is to have the possibility for sanity
        checks or conditional code evaluation which should not confuse
        the users when they work with the extracted code.

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

     Florian Hahne

