Interactive reports in R with knitr and RStudio

googleVis_with_knitr_and_RStudio.Rmd

My first examples with [***knitr***](http://yihui.name/knitr/)
-----------------------------------------
Let's include some simple R code:
```{r}
1+2
```
That worked.

Let's include a plot:
```{r fig.width=4, fig.height=4}
df <- data.frame(x=1:10, y=1:10)
plot(y ~ x, data=df, pch=19, col="blue")
```
Nice. 

Now let's insert an interactive chart with [***googleVis***](http://code.google.com/p/google-motion-charts-with-r):
```{r}
## load the googleVis package
suppressPackageStartupMessages(library(googleVis))
## create the scatter chart
sc <- gvisScatterChart(data=df,
                        options=list(width=300, height=300, 
                                     legend='none',
                                     hAxis="{title:'x'}",
                                     vAxis="{title:'y'}")

          )
```
The output of *gvisScatterChart* is a complete web page, including \<html\> and \<body\> tags, but here I only need the chart itself which is stored in *sc\$html\$chart*. To include the chart in the output we have to set the *result* parameter for the code chunk to *'asis'*, or otherwise the html code generated by *googleVis* will be displayed as a string.
```{r results='asis'}
## {r results='asis'}
print(sc, 'chart') ## same as cat(sc$html$chart)
```
Hurray, it works! Hover over the dots to get more information about the values. I am sure this could be simplified further in the same way that I can use *ggplot2* and *lattice* plots without the explicit print statement.

Next, let's create a geo chart: 
```{r results='asis'}
geo <- gvisGeoChart(CityPopularity, locationvar='City', 
                  colorvar='Popularity',
                    options=list(region='US', height=350, 
                                   displayMode='markers',
  			   colorAxis="{colors: ['orange','blue']}") )
print(geo, 'chart')
```
Wonderful! 

Unfortunately for charts which still rely on Flash, such as *gvisMotionChart, gvisAnnotatedTimeLine* and *gvisGeoMap*, the preview browser of RStudio will not display those charts at the moment. You have to open the output html-file in your system browser. But that is easy, just hit the browser button in the preview window, circled in red below.

![RStudio preview window](http://3.bp.blogspot.com/-b7iTQkXybNI/T7KtgqtE0_I/AAAAAAAAARY/Q_ZyViiQBrg/s1600/Untitled.png)

Additionally you may have to add your working directory to the trusted location in the [global secturity settings](http://www.macromedia.com/support/documentation/en/flashplayer/help/settings_manager04.html) of your Flash Player.

Here is a little motion chart example:
```{r results='asis'}
M <- gvisMotionChart(Fruits, "Fruit", "Year",
                     options=list(width=550, height=450))
print(M, 'chart')
```
Conclusion
-----------

RStudio and *knitr* might be the way forward to create quick analysis reports.

The markdown language should be sufficient for most tasks to draft a report, and the integration with RStudio makes it a real pleasure to work with *knitr*.

Unfortunately a spell checker is currently missing for knitr files, but I wouldn't be surprised if this will be added to a future version of RStudio.