controlling_knitr.Rmd

Controlling knitr output
========================================================
You can control what is output from code chunks by changing knitr options.
options are described [here](http://yihui.name/knitr/options) in detail.

Below some of the options I most use are shown.


Code evaluation
-------------------------
`eval=FALSE` will turn the code evaluation off. The code still will be shown.
  
with `eval=TRUE`
```{r}
summary(cars)
```
with `eval=FALSE`
```{r,eval=FALSE}
summary(cars)
```


Supressing warnings
-------------------------
You can supress warnings in the code output by setting `warning=FALSE`

`warning=TRUE`
```{r}
cor(c(1,1,1),c(1,1,1))
```

`warning=FALSE`
```{r,warning=FALSE}
cor(c(1,1,1),c(1,1,1))
```

Supressing messages
-------------------------
You can suppress messages from the code by setting `message=FALSE`

`message=TRUE`
```{r}
library(GenomicRanges)
```

`message=FALSE` for the R chunk.
```{r,message=FALSE}
library(GenomicRanges)
```


Evaluate code but hide figures
-------------------------

  
```{r fig.width=7, fig.height=6}
plot(cars)
```

You can also execute code but hide the figures with `fig.show='hide'` option for the R chunk.

```{r fig.width=7, fig.height=6,fig.show='hide'}
plot(cars)
summary(cars)
```