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| --- | ||
| title: "Discovering regulated Metabolite Families" | ||
| author: | ||
| - name: Khabat Vahabi | ||
| affiliation: Leibniz Institute of Plant Biochemistry | ||
| - name: Steffen Neumann | ||
| affiliation: Second Author's Affiliation | ||
| email: [email protected] | ||
| package: MetFamily | ||
| output: | ||
| BiocStyle::html_document | ||
| abstract: | | ||
| Description of your vignette | ||
| vignette: | | ||
| %\VignetteIndexEntry{Vignette Title} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| %\VignetteEncoding{UTF-8} | ||
| --- | ||
|
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| # Getting started | ||
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| To enable the _Bioconductor_ style in your R Markdown vignette you need to include the following in the `DESCRIPTION` file: | ||
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| VignetteBuilder: knitr | ||
| Suggests: BiocStyle, knitr, rmarkdown | ||
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| # Style macros | ||
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| _BiocStyle_ introduces the following macros for referring to _R_ packages: | ||
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| * `r Biocpkg("IRanges")`, for _Bioconductor_ software, annotation and experiment data packages, | ||
| * `r CRANpkg("data.table")`, for _R_ packages available on CRAN, | ||
| * `r Githubpkg("rstudio/rmarkdown")`, for _R_ packages available on GitHub, | ||
| * `r Rpackage("MyPkg")`, for _R_ packages that are _not_ available on _Bioconductor_, CRAN or GitHub. | ||
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| # Figures | ||
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| Assign captions to figures in the code chunk option `fig.cap` to automatically number them, and to be able to reference them, see Figure \@ref(fig:plot). The figure label is generated from the code chunk label by prefixing it with `fig:`. | ||
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| ```{r plot, fig.cap="Regular figure. The first sentence of the figure caption is automatically emphasized to serve as figure title.", echo=FALSE} | ||
| plot(cars) | ||
| ``` | ||
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| Small and wide figures can be specified by `fig.small` and `fig.wide` code chunk options. | ||
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| ```{r small, fig.cap="Small figure. A plot produced by a code chunk with option `fig.small = TRUE`.", fig.small=TRUE, echo=FALSE} | ||
| plot(cars) | ||
| ``` | ||
| ```{r wide, fig.cap="Wide figure. A plot produced by a code chunk with option `fig.wide = TRUE`.", fig.wide=TRUE, echo=FALSE} | ||
| plot(cars) | ||
| ``` | ||
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| # Equations | ||
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| To number and reference equations, put them in equation environments and assign labels to them, see Equation \@ref(eq:binom). | ||
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| \begin{equation} | ||
| f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k} | ||
| (\#eq:binom) | ||
| \end{equation} | ||
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| # Tables | ||
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| Like figures, tables with captions will also be numbered and can be referenced, see Table \@ref(tab:table). | ||
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| Fruit | Price | ||
| ------- | ----- | ||
| bananas | 1.2 | ||
| apples | 1.0 | ||
| oranges | 2.5 | ||
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| : (\#tab:table) A simple table. With caption. | ||
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| # Cross-references | ||
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| Apart from referencing figures (Section \@ref(figures)), tables (Section \@ref(tables)), and equations (Section \@ref(equations)), you can also use the same syntax to refer to sections by their default labels generated by pandoc. | ||
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| # Side notes | ||
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| Footnotes are displayed as side notes on the right margin^[this is a side note entered as a footnote], which has the advantage that they appear close to the place where they are defined. | ||
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| # Session info {.unnumbered} | ||
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| ```{r sessionInfo, echo=FALSE} | ||
| sessionInfo() | ||
| ``` |