Cambridge R user meeting, May 2012

Cambridge_R_googleVis_with_knitr_and_RStudio_May_2012.Rmd

Interactive charts and slides with R, googleVis and knitr
========================================
```{r results='asis', echo=FALSE, message=FALSE, tidy=FALSE}
library(googleVis)
G <- gvisGeoChart(Exports, "Country", "Profit", 
                  options=list(width=250, height=120), chartid="c1")

T <- gvisBarChart(Exports[,1:2], yvar="Profit", xvar="Country",                  
                  options=list(width=250, height=260, 
                               legend='none'), chartid="c2")

GT <- gvisMerge(G,T, horizontal=FALSE, chartid="gt") 

## Tree map

M <- gvisTreeMap(Regions,  "Region", "Parent", "Val", "Fac",
                    options=list(width=400, height=380,
                                 fontSize=16,
                                 minColor='#EDF8FB',
                                 midColor='#66C2A4',
                                 maxColor='#006D2C',
                                 headerHeight=20,
                                 fontColor='black',
                                 showScale=TRUE), chartid="c3")

GTM <- gvisMerge(GT, M, horizontal=TRUE,
                     tableOptions="cellspacing=5", chartid="gtm")

print(GTM, 'chart')
```
[Markus Gesmann](https://plus.google.com/118201313972528070577/posts), [Cambridge R user group](http://www.cambr.org.uk/) meeting, 29 May 2012

# Agenda
* Motivation
* Introduction to googleVis
* Examples with googleVis
* How I created this talk with RStudio, knitr, pandoc and slidy

# Motivation
<iframe width="420" height="315" src="http://www.youtube.com/embed/hVimVzgtD6w" frameborder="0" allowfullscreen></iframe>

* In 2006 Hans Rosling gave an inspiring talk at TED 
* He challenged the views and perceptions of many listeners
* To visualise his talk he used animated bubble charts, aka motion charts

# Google Chart Tools

* Google integrated the motion charts into their [Visualisation API](https://developers.google.com/chart/) in 2007
* Google Visulisation API makes it easy to create interactive charts for web pages 
* It uses JavaScript and DataTable / JSON as input
* Output is either HTML5/SVG or Flash
* Browser with internet connection required to display chart
* Please read the Google [Terms of Service](https://developers.google.com/terms/) before you start

# Introduction to googleVis
* [googleVis](http://code.google.com/p/google-motion-charts-with-r/) is a package for [R](http://www.r-poject.org/) and provides an interface between R and the [Google Chart Tools](https://developers.google.com/chart/), see *Using the Google Visualisation API with R*, 
  [The R Journal, 3(2):40-44, December 2011](http://journal.r-project.org/archive/2011-2/RJournal_2011-2_Gesmann+de~Castillo.pd)
* The functions of the package allow users to visualise data with the Google Chart Tools without uploading their data to Google
* The output of googleVis functions is html code that contains the data and references to JavaScript functions hosted by Google
* To view the output a browser with an internet connection is required, the actual chart is rendered in the browser; some charts require Flash

# Key ideas of googleVis
* Create wrapper function in R which generate html files with references to Google's Chart Tools API
* Transform R data frames into [JSON](http://www.json.org/) objects with [RJSONIO](http://www.omegahat.org/RJSONIO/)
```{r}
cat(toJSON(CityPopularity)) ## example data from googleVis
```

* Display the HTML output with the R HTTP help server
* Development started in August 2010, intially to visualise data at [Lloyd's](http://www.lloyds.com/The-Market/Tools-and-Resources/Resources/Statistics-Relating-to-Lloyds/Visualisation)

# googleVis version 0.2.16 provides interfaces to 

* Motion Charts
* Annotated Time Lines
* Maps, Geo Maps and Charts
* Intensity Maps
* Tables, Gauges, Tree Maps
* Line-, Bar-, Column-, Area- and Combo Charts
* Scatter-, Bubble-, Candlestick-, Pie- and Org Charts

Run ```demo(googleVis)``` to see [examples](http://code.google.com/p/google-motion-charts-with-r/wiki/GadgetExamples) of all charts and read the [vignette](http://cran.r-project.org/web/packages/googleVis/vignettes/googleVis.pdf) for more details.

# [World Bank example](http://lamages.blogspot.co.uk/2011/09/accessing-and-plotting-world-bank-data.html)
<iframe height="550px" frameborder="no" scrolling="no"
src="http://dl.dropbox.com/u/7586336/blogger/WorldBankMotionChart.html"
width="100%">
</iframe>
```{r eval=FALSE}
library(googleVis)
demo(WorldBank) 
```


# Video tutorial

<iframe width="420" height="315" src="http://www.youtube.com/embed/Z6NYQdiwTrU" frameborder="0" allowfullscreen></iframe>

* Video tutorial by [Martin Hilpert](http://omnibus.uni-freiburg.de/~mh608/), [Freiburg Institute for Advanced Studies](http://www.frias.uni-freiburg.de/)
* Demonstrates how to create motion charts with googleVis


# The googleVis concept

* Charts: *'gvis' + ChartType*
* For a motion chart we have
```{r eval=FALSE}
M <- gvisMotionChart(data, idvar='id', timevar='date', options=list(), chartid)
```
* Output of googleVis is a list of list
* Display the chart by simply plotting the output ```plot(M)```
  * Plot will generate a temporay html-file and open it in a new browser window 
* Specific parts can be extracted, e.g. the chart ```M$html$chart``` or data ```M$html$chart["jsData"]```

# Embedding googleVis chart into your web page

Suppose you have an existing web page and would like to integrate the output of a googleVis function, such as ```gvisMotionChart```.

In this case you only need the chart output from ```gvisMotionChart```. So you can either copy and paste the output from the R console

```{r eval=FALSE}
 print(M, 'chart') ## or cat(M$html$chart)
```
into your existing html page, or write the content directly into a file

```{r eval=FALSE}
print(M, 'chart', file='myfilename')
```
and process it from there.


# Simple line chart
```{r results='asis'}
df <- data.frame(label=c("A", "B", "C"), val1=c(0.10,0.13,0.14), val2=c(23,12,32))
lc <- gvisLineChart(df)
print(lc, 'chart') ## So knitr includes the html output of the chart 
```


# Line chart with options set
```{r results='asis'}
print(gvisLineChart(df, xvar="label", yvar=c("val1","val2"),
                        options=list(title="Hello World", legend="bottom",
                          titleTextStyle="{color:'red', fontSize:18}",                         
                          vAxis="{gridlines:{color:'red', count:3}}",
                          hAxis="{title:'My Label', titleTextStyle:{color:'blue'}}",
                          series="[{color:'green', targetAxisIndex: 0}, 
                                   {color: 'blue',targetAxisIndex:1}]",
                          vAxes="[{title:'Value 1 (%)', format:'#,###%'}, 
                                  {title:'Value 2 (\U00A3)'}]",                          
                          curveType="function", width=500, height=300                         
                          )), 'chart')
```

# Chart countries' S&P credit rating
* Plot countries' S&P credit rating sourced from Wikipedia
* See my [blog post](http://lamages.blogspot.co.uk/2012/01/credit-rating-by-country.html) for more details
```{r}
## Get and prepare data
library(XML)
url <- "http://en.wikipedia.org/wiki/List_of_countries_by_credit_rating"
page <- readLines(url)
x <- readHTMLTable(page, which=3)
levels(x$Rating) <- substring(levels(x$Rating), 4, 
                            nchar(levels(x$Rating)))
x$Ranking <- x$Rating
levels(x$Ranking) <- nlevels(x$Rating):1
x$Ranking <- as.character(x$Ranking)
x$Rating <- paste(x$Country, x$Rating, sep=": ")
```

# Chart countries' S&P credit rating
```{r results='asis'}
print(gvisGeoMap(x, "Country", "Ranking", "Rating",
                  options=list(gvis.editor="S&P", 
                  colors="[0x91BFDB, 0XFC8D59]")), 'chart')
```

# Geo chart with markers
```{r results='asis'}
require(stats)
data(quakes); quakes$latlong<-paste(quakes$lat, quakes$long, sep=":")
print(gvisGeoChart(quakes, locationvar="latlong", colorvar="depth", sizevar="mag",
                   options=list(displayMode="Markers", region="009",
                   colorAxis="{colors:['red', 'grey']}",
                   backgroundColor="lightblue")), 'chart')
```

# Merging gvis-objects

```{r results='asis'}
G <- gvisGeoChart(Exports, "Country", "Profit", options=list(width=250, height=120))
B <- gvisBarChart(Exports[,1:2], yvar="Profit", xvar="Country",                  
                  options=list(width=250, height=260, legend='none'))
M <- gvisMotionChart(Fruits, "Fruit", "Year",options=list(width=400, height=380))
GBM <- gvisMerge(gvisMerge(G,B, horizontal=FALSE), 
                 M, horizontal=TRUE, tableOptions="cellspacing=5")
print(GBM, 'chart')
```


# Further case studies

* [Statistics Relating to Lloyd's](http://www.lloyds.com/The-Market/Tools-and-Resources/Resources/Statistics-Relating-to-Lloyds/Visualisation)
* [Analysis of the US domestic airline market from 1999 - 2010](http://www.cambridge.aero/_blog/main/post/US_Domestic_Airline_Market_In_Motion_1990-2010/)
* [Linguistic analysis of the English language](http://omnibus.uni-freiburg.de/~mh608/motion.html)
* [Exploring the Pen World Data](http://usefulr.wordpress.com/2012/04/17/quickly-explore-the-penn-world-tables-in-r/)
* [My blog posts on googleVis](http://lamages.blogspot.co.uk/search/label/googleVis)

# Other R packages

* [R animation package allows to create SWF, GIF and MPEG directly](http://animation.yihui.name/)
* [iplots: iPlots - interactive graphics for R](http://cran.r-project.org/web/packages/iplots/)
* [Acinonyx aka iPlots eXtreme](http://rforge.net/Acinonyx/index.html)
* [gridSVG: Export grid graphics as SVG](http://cran.r-project.org/web/packages/gridSVG/index.html)
* [plotGoogleMaps: Plot HTML output with Google Maps API and your own data](http://cran.r-project.org/web/packages/plotGoogleMaps/)
* [RgoogleMaps: Overlays on Google map tiles in R](http://cran.r-project.org/web/packages/RgoogleMaps/index.html)

# How I created this presentation with RStudio, knitr, pandoc and slidy  
* [knitr](http://yihui.name/knitr/) is a package by [Yihui Xie](http://yihui.name/) that brings literate programming to a new level 
  * It allows to create content really quickly, without worrying to much about layout and R formatting
* [RStudio](http://rstudio.org) integrated knitr into its IDE, which allows to knit Rmd-files by the push of a button into markdown
* Markdown output can be converted into serveral other file formats, such as html, with [pandoc](http://johnmacfarlane.net/pandoc/)
* [slidy](http://www.w3.org/Talks/Tools/Slidy2/Overview.html) is one of the options to create interactive html-slides with pandoc

```
pandoc -s -S -i -t slidy --mathjax 
  Cambridge_R_googleVis_with_knitr_and_RStudio_May_2012.md 
  -o Cambridge_R_googleVis_with_knitr_and_RStudio_May_2012.html
```

* For more details see my recent [blog post](http://lamages.blogspot.co.uk/2012/05/interactive-reports-in-r-with-knitr-and.html) and [example file](https://gist.github.com/2704646)
* The source file of this presentation is available on [github](https://gist.github.com/2816027)

# Conclusion

* Interactive charts and reports open a new way to engage with readers and users, who would find data and figures boring otherwise
* RStudio, *knitr* and googleVis might be the way forward to create interactive analysis reports and presentations
* The markdown language should be sufficient for most tasks to draft a report, and the integration with RStudio makes it a pleasure to work with *knitr*.

# Thanks to ...

* Google for making the Chart Tools available 
* My co-author Diego de Castillo
* [All who have provided ideas, feedback, bug reports, suggestions, etc.](http://google-motion-charts-with-r.googlecode.com/svn/trunk/THANKS)
* [Yihui Xie](http://yihui.name/) for [knitr](http://yihui.name/knitr/)
* JJ, Joe and Josh for [RStudio](http://rstudio.org/)
* [Dave Raggett](http://www.w3.org/People/Raggett/) for [Slidy](http://www.w3.org/Talks/Tools/Slidy2)

# Contact
* googleVis: [http://code.google.com/p/google-motion-charts-with-r/](http://code.google.com/p/google-motion-charts-with-r/)
* My blog: [http://lamages.blogspot.co.uk/](http://lamages.blogspot.co.uk/)
* Email: markus dot gesmann at gmail dot com

Getting error in line 66 in running from Rstudio (version .99) on R 3.2.0

cat(toJSON(CityPopularity)) ## example data from googleVis

could not find toJSON call withCallingHandlers->withVisible_> eval->eval->cat