R visualization: ggplot2, googlevis, plotly, igraph Overview

DataVisualization in

R

Olga Scrivner

ggplot2

googleVis

plotly

igraphData Visualization in R

Olga Scrivner


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Outline

1. ggplot2 (Hadley Wickham)

2. googleVis

3. plotly

4. igraph


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

R Package - ggplot2

I Advantages

I flexible

I plot specification at a level of abstraction

I themes

I Things you cannot do with ggplot2

I 3D and interactive graphics

I network graphs (nodes/edges)

I Some resources:

I http://tutorials.iq.harvard.edu/R/Rgraphics/Rgraphics.html

I Intro http://heather.cs.ucdavis.edu/~matloff/GGPlot2/GGPlot2Intro.pdf

http://tutorials.iq.harvard.edu/R/Rgraphics/Rgraphics.htmlhttp://tutorials.iq.harvard.edu/R/Rgraphics/Rgraphics.htmlhttp://heather.cs.ucdavis.edu/~matloff/GGPlot2/GGPlot2Intro.pdfhttp://heather.cs.ucdavis.edu/~matloff/GGPlot2/GGPlot2Intro.pdf


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Grammar of Graphics - Independent Blocks

a) Object initialization

I ggplot(data, mapping=aes() )

b) Aesthetic mapping (aes)

I Describes how variables in the data are mapped tovisual properties (aesthetics) of geoms

I aes(x = mpg, y = wt)

c) Geoms - geometric objects

I geom_bar; geom_boxplot; geom_histogram

I Plot must have at least one geom


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Materials

1. Download: landdata-states.csv

2. Script week4.r

Materials are based on tutorialhttp://tutorials.iq.harvard.edu/R/Rgraphics/

http://tutorials.iq.harvard.edu/R/Rgraphics/


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Basic Graphics - Histogram

hist(mydata$Home.Value)


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Ggplot

1st Block: Object initialization

p


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

AES(x,y)

p


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Points: Shape, Size, Color

Shape: 25 symbolsa data frame with three columns:df


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Lines: geom_line

0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash,5 = longdash, 6 = twodash

df2


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Lines: geom_line

I Change line type

I Add size

I Add color

I f + geom_line(linetype = 3, size = 4, color = red)


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Smoother: geom_smooth()

Lets select HAWAII from mydata:

mydata[State ==HI, ]

attach(mydata)p


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Conditions

& means AND

| means OR

How would you extract two states HAWAII and DC frommydata? AND or OR?

mydata[State == HI | State == DC ,]

p


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Scale

I One scale per aesthetic (AES)


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Theme

I Handles non-data plot elements (axis, legend,background)

I Built-in themesI theme_grey()I theme_classic()I theme_dark()I theme_light()

Add to your last line:

p + geom_point() + geom_smooth() + theme_classic()


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

What is googleVis?

I Interface between R and the Google Charts API

I Google Charts - interactive charts that can be embeddedinto web pages

I Hans Rosling in TED talk 2006

I Internet connection

I Flash player is required for some charts

https://www.ted.com/talks/hans_rosling_shows_the_best_stats_you_ve_ever_seen

https://www.ted.com/talks/hans_rosling_shows_the_best_stats_you_ve_ever_seenhttps://www.ted.com/talks/hans_rosling_shows_the_best_stats_you_ve_ever_seen


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Chart Types

1. Motion Charts gvisMotionChart()2. Annotated time lines gvisTimeline()3. Maps gvisMap()4. Other (line, bubble, area etc)5. Output is HTML code with data and references to

JavaScript


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Google Chart Structure

Markus Gesmann and Diego de Castillo. 2017. Introduction togoogleVis 0.6.2


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Motion Chart

demo(WorldBank)


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Enable Flash Player - Chrome

1. In address bar chrome:plugins2. Check the status: Enable

3. Select Always allowed to run


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Motion Chart

head(Fruits)Motion=gvisMotionChart(Fruits,idvar="Fruit",timevar="Year")

plot(Motion)


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

User Guide


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Plotly

1. Plotly - a collaborative business intelligence platform

2. Plotlys R library makes interactive graphs3. Plotly uses the htmlwidget framework that works in

various contexts (R Markdown documents, shiny apps,inside RStudio, Jupiter Notebook) without an internetconnection

Lavf56.36.100

collaboration.mp4Media File (video/mp4)


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Resources

Resources:I https://cpsievert.github.io/plotly_book/I https://plot.ly/r/I https://plot.ly/ggplot2/

https://cpsievert.github.io/plotly_book/https://plot.ly/r/https://plot.ly/ggplot2/


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Ggplot Integration

Plotly package provides ggplotly() converting a ggplotobject to a plotly object

http://ropensci.github.io/plotly/ggplot2/

http://ropensci.github.io/plotly/ggplot2/


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Usage

Click on the bar graph!


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Usage - Export


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

ggplotly()

Lets revisit mydata

attach(mydata)p


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Publishing

1. Select Publish HTML

2. Select RStudio account or RPubs

3. Publish!


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Two Approaches

1. ggplotly() function

I Converting ggplot objects into plotly objects

I Requires data frames

2. plot_ly() interface

I Flexible interface to plotly.js

I Can use data frames and matrices


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

plot_ly()

head(volcano)x


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Standalone Web Page

1. Save as Web page

2. View 3D volcano web page


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

PCA and Cluster in plotly

PCA: principal component analysis

We are going to build this interactive plot (credits - JiviteshPoojary)

More resources on PCA:https://tgmstat.wordpress.com/2013/11/28/computing-and-visualizing-pca-in-r/

https://tgmstat.wordpress.com/2013/11/28/computing-and-visualizing-pca-in-r/https://tgmstat.wordpress.com/2013/11/28/computing-and-visualizing-pca-in-r/


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

PCA

Download R code for PCA and Cluster from Canvas

pcaCars


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

PCA - Cluster Code

# add cluster to data frame of scorescarsDf


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

igraph - Network

Canvas: igraph workshop material (NetSciX 2016 School ofCode Workshop)

I Undirected graph with three edgesI Numbers are vertex IDsI Edges are: 1 2, 2 3, 3 1


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Graphs

library(igraph)g1


R

Olga Scrivner

ggplot2

googleVis

plotly

igraph

Credits

https://community.uservoice.com/blog/data-visualization-best-practices/https://opr.princeton.edu/workshops/Downloads/2015Jan_ggplot2Koffman.pdf NetSciX 2016 School of CodeWorkshop

https://community.uservoice.com/blog/data-visualization-best-practices/https://community.uservoice.com/blog/data-visualization-best-practices/https://opr.princeton.edu/workshops/Downloads/2015Jan_ggplot2Koffman.pdfhttps://opr.princeton.edu/workshops/Downloads/2015Jan_ggplot2Koffman.pdf

ggplot2googleVisplotlyigraph

R visualization: ggplot2, googlevis, plotly, igraph Overview

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