example knitr.r

knitr.rmd

### KNITR SETUP

```{r setup, echo=FALSE}
opts_chunk$set(tidy=TRUE, cache=FALSE, highlight=TRUE, figalign="center", warning=FALSE,  error=FALSE, message=FALSE, fig.height=11, fig.width=11)
```

### EXAMPLE CHUNK
```{r libraries}
library(ggplot2)
library(xtable)
```

### EXAMPLE ggplot generation and printing

```{r generate_plot}
colors <- factor(df$foo)
p <- ggplot(data=df, aes(x=xval, y=-log10(yval), label=symbol, color=colors)) + geom_point(size=8, alpha=0.7) + scale_colour_discrete(name = "legend title") + xlab("xlab") + ylab("ylab") 
```

#### print out plot

```{r print_plot, fig.cap="figure legend"}
print(p)
```

### EXAMPLE table generation and printing

#### Table1 - Table title

```{r table, results='asis'}
table1 <- xtable(df, label=NULL, digits=c(1,1,1,6,0,1)) ## here you have 6 columns and "digits = the number of digits to round to for each column 
print(table1, type="html",include.rownames=FALSE)
```