markup {BiocCaseStudies} | R Documentation |
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
:solution
:myincfig
:solfig
:myref
:booklab
:The following makros will automatically create index entries as side effect. Apart from that they do text highlighting as well.
R
:Rpackage
:Rclass
:Rmethod
:Rfunction
:Implicit index terms can be generated using
indexTerm
: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:
Robject
:Rfunarg
:code
:term
:\{emph}
is set tofile
:reg
:The following environments are used to structure the document and for parsing . They do not impose any layout.
chapterheader
:chapterbody:
chaptertrailer:
yaa
:input
also setting the
graphics include path. Its first parameter is filename, second
parameter is graphics pathColor and options
BiocCaseStudies
as objects
lcol1
, lcol2
and lcol3
for light colors, and
dcol1
, dcol2
and dcol3
for dark colors.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.Florian Hahne