vignettes/sitt.md

In taylo5jm/interactions: Classification of gene expression profile sets generated from combination stimuli

title: "sitt: Signal Interaction Tools for Transcriptomics" author: "Justin Taylor" date: "2015-08-28" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc}

Vignette Info

Note the various macros within the vignette setion of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Styles

The html_vignette template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:

output:
  rmarkdown::html_vignette:
    css: mystyles.css

Figures

The figure sizes have been customised so that you can easily put two images side-by-side.

plot(1:10)
plot(10:1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

More Examples

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

| | mpg| cyl| disp| hp| drat| wt| qsec| vs| am| gear| carb| |:-----------------|----:|---:|-----:|---:|----:|-----:|-----:|--:|--:|----:|----:| |Mazda RX4 | 21.0| 6| 160.0| 110| 3.90| 2.620| 16.46| 0| 1| 4| 4| |Mazda RX4 Wag | 21.0| 6| 160.0| 110| 3.90| 2.875| 17.02| 0| 1| 4| 4| |Datsun 710 | 22.8| 4| 108.0| 93| 3.85| 2.320| 18.61| 1| 1| 4| 1| |Hornet 4 Drive | 21.4| 6| 258.0| 110| 3.08| 3.215| 19.44| 1| 0| 3| 1| |Hornet Sportabout | 18.7| 8| 360.0| 175| 3.15| 3.440| 17.02| 0| 0| 3| 2| |Valiant | 18.1| 6| 225.0| 105| 2.76| 3.460| 20.22| 1| 0| 3| 1| |Duster 360 | 14.3| 8| 360.0| 245| 3.21| 3.570| 15.84| 0| 0| 3| 4| |Merc 240D | 24.4| 4| 146.7| 62| 3.69| 3.190| 20.00| 1| 0| 4| 2| |Merc 230 | 22.8| 4| 140.8| 95| 3.92| 3.150| 22.90| 1| 0| 4| 2| |Merc 280 | 19.2| 6| 167.6| 123| 3.92| 3.440| 18.30| 1| 0| 4| 4|

Also a quote using >:

"He who gives up [code] safety for [code] speed deserves neither." (via)

taylo5jm/interactions documentation built on May 31, 2019, 3:57 a.m.