Posts Tagged ‘ visualization ’

One datavis for you, ten for me

September 14, 2014
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One datavis for you, ten for me

Over the years of my graduate studies I made a lot of plots. I mean tonnes. To get an extremely conservative estimate I grep’ed for every instance of “plot\(” in all of the many R scripts I wrote over the past five years. The actual number is very likely orders of magnitude larger as 1) many […]

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Plot with ggplot2, interact, collaborate, and share online

July 31, 2014
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Plot with ggplot2, interact, collaborate, and share online

Editor’s note: This is a guest post by Marianne Corvellec from Plotly. This post is based on an interactive Notebook (click to view) she presented at the R User Conference on July 1st, 2014. Plotly is a platform for making, editing, and sharing graphs. If you are used to making plots with ggplot2, you can […]

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Using Volcano Plots in R to Visualize Microarray and RNA-seq Results

May 28, 2014
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Using Volcano Plots in R to Visualize Microarray and RNA-seq Results

I've been asked a few times how to make a so-called volcano plot from gene expression results. A volcano plot typically plots some measure of effect on the x-axis (typically the fold change) and the statistical significance on the y-axis (typically the...

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qqman: an R package for creating Q-Q and manhattan plots from GWAS results

May 15, 2014
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qqman: an R package for creating Q-Q and manhattan plots from GWAS results

Three years ago I wrote a blog post on how to create manhattan plots in R. After hundreds of comments pointing out bugs and other issues, I've finally cleaned up this code and turned it into an R package.The qqman R package is on CRAN: http://cran.r-project.org/web/packages/qqman/The source code is on GitHub: https://github.com/stephenturner/qqmanIf you'd like to cite the qqman package (appreciated but not required), please cite this pre-print: Turner, S.D. qqman: an R package…

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Exploring US healthcare data

April 13, 2014
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Exploring US healthcare data

A few days ago, the Centers for Medicare and Medicaid Services (CMS) released some unprecedented data on the US healthcare system. The data consists of 9 million rows showing how much each doctor in the US charged Medicare, for what, and how much Medicare paid out. It doesn't quite cover everything (for example, services with less than 11 beneficiaries were removed for privacy reasons), but its the best thing we've…

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Shape File Selfies in ggplot2

April 12, 2014
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Shape File Selfies in ggplot2

In this post you will learn how to: Create your own quasi-shape file Plot your homemade quasi-shape file in ggplot2 Add an external svg/ps graphic to a plot Change a grid grob's color and alpha *Note get simple .md version … Continue reading →

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Visualize coverage for targeted NGS (exome) experiments

March 20, 2014
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Visualize coverage for targeted NGS (exome) experiments

I'm calling variants from exome sequencing data and I need to evaluate the efficiency of the capture and the coverage along the target regions.This sounds like a great use case for bedtools, your swiss-army knife for genomic arithmetic and interval man...

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Sochi Olympic Medals

February 9, 2014
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Sochi Olympic Medals

For those who are addicted to R and haven’t the time to click the mouse on a web browser you too can still be informed about the results of the 2014 Sochi Winter Olympics. I was inspired by a SO … Continue reading →

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Online R and Plotly Graphs: Canadian and U.S. Maps, Old Faithful with Multiple Axes, & Overlaid Histograms

February 6, 2014
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Online R and Plotly Graphs: Canadian and U.S. Maps, Old Faithful with Multiple Axes, & Overlaid Histograms

Guest post by Matt Sundquist of plot.ly. Plotly is a social graphing and analytics platform. Plotly’s R library lets you make and share publication-quality graphs online. Your work belongs to you, you control privacy and sharing, and public use is free (like GitHub). We are in beta, and would love your feedback, thoughts, and advice. […]

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The Extra Step: Graphs for Communication versus Exploration

January 12, 2014
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The Extra Step: Graphs for Communication versus Exploration

Visualization is a useful tool for data exploration and statistical analysis, and it’s an important method for communicating your discoveries to others. While those two uses of visualization are related, they aren’t identical. One of the reasons that I like ggplot so much is that it excels at layering together multiple views and summaries of […] Related posts: Revisiting Cleveland’s The Elements of Graphing Data in ggplot2 My Favorite Graphs…

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