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': makro for figure environments with three parameters: (1)
     figure filename (2) figure width (3) figure caption

'_s_o_l_f_i_g': makro 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

