Whether you use circles as visual encodings or as a way to highlight areas of a plot, there are functions at your disposal.
R

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Drawing Circles and Ellipses in R

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Drawing Squares and Rectangles in R
R makes it easy to add squares and rectangles to your plots, but it gets a little tricky when you have a bunch to draw at once. The key is to break it down to the elements.

Voronoi Diagram and Delaunay Triangulation in R
The
deldir
package by Rolf Turner makes the calculations and plotting straightforward, with a few lines of code. 
Comparing ggplot2 and R Base Graphics
Figure out which is best with a sidebyside comparison.

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Adding Legends in R
Make sure you explain your visual encodings so that others can interpret them.

Emergency room data in R
For my graphic on emergency room visits over time and the other on things that get stuck, I used data from the National Electronic Injury Surveillance System, which is maintained…

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How to Customize Axes in R
For presentation purposes, it can be useful to adjust the style of your axes and reference lines for readability. It's all about the details.

R growth on StackOverflow reigns supreme
Joshua Kunst did a quick analysis on tag usage on StackOverflow, the question and answer site for programming. The R tag isn’t the top of course, but it is growing…

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Animated Pyramid Chart in R
Make a bunch of charts, string them together like a flip book, and there's your animation. Sometimes good for showing changes over time. Always fun to play with.

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Bivariate Area Charts in R
Quickly compare two time series variables with this linearea chart hybrid that originated in the 1700s.

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How to Make Maps in R That Include Alaska and Hawaii
The conterminous United States always gets the attention, while Alaska and Hawaii are often left out. It is time to bring them back into view.

Tufte style charts in R
Lukasz Piwek is chipping away at a collection of Tuftestyle charts using R, along with the code snippets. Fittingly, the project is called Tufte in R. The Tufte stuff is…

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How to Map and Use GeoTIFF Files in R
It's like working with a bunch of tiny dots, and oh look, all of sudden patterns emerge.

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How to Make Horizon Graphs in R
The relatively new and lesser known time series visualization can be useful if you know what you're looking at, and they take up a lot less space.

R Consortium for further development of community
The Linux Foundation announced the R Consortium to provide support to the R Foundation and to organizations developing the language. “Millions of data scientists and academic researchers use R language…

Working with R at the New York Times
Amanda Cox from the New York Times was on the Data Stories podcast. You should listen. She talks about how she uses R, workflow at the New York Times, and…

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How to Make Variable Width Bar Charts in R
The code to create these bar chart variations is almost the same as if you were to make a standard bar chart. But make sure you get the math right.

R is quirky, flawed, and an enormous success
Most people who use R on the regular learned the language in the context of a subject outside of programming. They learned R as they learned statistical methods, or they…

Length of the average master’s thesis
A while back beckmw found the average length of a dissertation for various fields of study, based on digital archives at the University of Minnesota. Here’s a followup to that…

A Course for Visualization in R, Taking You From Beginner to Advanced
Where to start? What to learn next? Here's a course to help take you from beginner to advanced.

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How to Make Dot Plots in R
It's easy to draw dots. The challenge is to make them meaningful and readable.

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How to Make Line Charts in R
Learn to draw lines wherever and however you want, and you've got yourself some flexibility.

htmlwidgets: Create interactive web charts in R
If you don’t want to bother with JavaScript but want to publish interactive graphics for the web or use interaction to explore your data, htmlwidgets might be for you.…

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R Cheat Sheet and Guide for Graphical Parameters
You can customize graphics in R with
par()
, but the docs are mostly text and just organized alphabetically. Here is a more visual reference, categorized by what you can change. Plus, a onepage printout. 
R site updated
The R site has a new face. It looked dated for years — maybe decades — so I’m glad it got a refresh (with further updates in the coming months…

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How to Make and Use Bar Charts in R
The chart type seems simple enough, but there sure are a lot of bad ones out there. Get yourself out of default mode.

rvest: R package to scrape web data
Inspired by the Python libraries RoboBrowser and BeautifulSoup, the rvest package by Hadley Wickham helps you scrape web data via R in a similar way. Parse tables into data frames,…

Loading Data and Basic Formatting in R
It might not be sexy, but you have to load your data and get it in the right format before you can visualize it. Here are the basics, which might be all you need.

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Choropleth Maps and Shapefiles in R
Fill those empty polygons with color, based on shapefile or external data.

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Working with Map Projections and Shapefiles in R
No need to settle for the mapping defaults in R. Apply map projections to show geographic data in a way most suitable for your work.