markup: Markup commands.
In BiocCaseStudies: BiocCaseStudies: Support for the Case Studies Monograph

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

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

Ex:environment for exercise chunks.
solution:environment for solutions to the exercises.
\myincfig:macro for figure environments with three parameters: (1) figure filename (2) figure width (3) figure caption
\solfig:macro for figure environments within solution chunks. This is necessary because LaTex doesn't allow for floats within minipage environments.
\myref: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.
\booklab: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.

Implicit index terms can be generated using

\indexTerm: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:

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

chapterheader:this contains title, authors and abstract of the chapter/lab
chapterbody:this contains the actual chapter body
chaptertrailer:this contains session info and references for a chapter
\yaa: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

colors: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.
Sweave options: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.