193 search results for "heatmap"

R for more powerful clustering

April 21, 2015
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R for more powerful clustering

by Vidisha Vachharajani Freelance Statistical Consultant R showcases several useful clustering tools, but the one that seems particularly powerful is the marriage of hierarchical clustering with a visual display of its results in a heatmap. The term “heatmap” is often confusing, making most wonder – which is it? A "colorful visual representation of data in a matrix" or "a...

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Project Tycho, ggplot2 and the shameless stealing of blog ideas

April 14, 2015
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Project Tycho, ggplot2 and the shameless stealing of blog ideas

Last week, Mick Watson posted a terrific article on using R to recreate the visualizations in this WSJ article on the impact of vaccination. Someone beat me to the obvious joke. @BioMickWatson @pathogenomenick Nice quilt plot. — Ed Yong (@edyong209) April 9, 2015 Someone also beat me to the standard response whenever base R graphics

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Analysing Dracula

April 14, 2015
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Analysing Dracula

I recently read Bram Stoker’s Dracula, mostly because I wanted to rewatch the 1990s movie of the same name and see how badly they’d mutilated the story.  [Update 26/04/2015: I rewatched the 1992 movie and while it’s the most faithful version to the book, it has some weird additions and is utterly appalling.  People have been … Continue reading...

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Six Ways You Can Make Beautiful Graphs (Like Your Favorite Journalists)

April 8, 2015
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Six Ways You Can Make Beautiful Graphs (Like Your Favorite Journalists)

This post shows how to make graphs like The Economist, New York Times, Vox, 538, Pew, and Quartz. And you can share–embed your beautiful, interactive graphs in apps, blog posts, and web sites. Read on to learn how. If you like interactive graphs and need to securely collaborate with your team, contact us about Plotly Enterprise.

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Using genomation to analyze methylation profiles from Roadmap epigenomics and ENCODE

March 31, 2015
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Using genomation to analyze methylation profiles from Roadmap epigenomics and ENCODE

The genomation package is a toolkit for annotation and visualization of various genomic data. The package is currently in developmental version of BioC. It allows to analyze high-throughput data, including bisulfite sequencing data. Here, we will visualize the distribution of CpG methylation around promoters and their locations within gene structures on human chromosome 3.Heatmap and...

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Another Interactive Map for the Cholera Dataset

March 31, 2015
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Another Interactive Map for the Cholera Dataset

Following my previous post, François (aka @FrancoisKeck) posted a comment mentionning another package I could use to get an interactive map, the rleafmap package. And the heatmap was here easy to include. This time, we do not use openstreetmap. The first part is still the same, to get the data, > require(rleafmap) > library(sp) > library(rgdal) > library(maptools) >...

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Interactive Maps for John Snow’s Cholera Data

March 28, 2015
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Interactive Maps for John Snow’s Cholera Data

This week, in Istanbul, for the second training on data science, we’ve been discussing classification and regression models, but also visualisation. Including maps. And we did have a brief introduction to the  leaflet package, devtools::install_github("rstudio/leaflet") require(leaflet) To see what can be done with that package, we will use one more time the John Snow’s cholera dataset, discussed in previous...

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Color extraction with R

March 4, 2015
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Color extraction with R

Given all the attention the internet has given to the colors of this dress, I thought it would be interesting to look at the capabilities for extracting colors in R. R has a number of packages for importing images in various file formats, including PNG, JPG, TIFF, and BMP. (The readbitmap package works with all of these.) In each...

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Eight New Ideas From Data Visualization Experts

February 12, 2015
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Eight New Ideas From Data Visualization Experts

This post summarizes and visualizes eight key ideas we’ve heard from data visualization experts. Check out our first Case Study to learn more about using Plotly Enterprise on-premise, on your servers. To get started on free online graphing like in this post, check out our tutorials. Make Interactive Graphs Pictures of graphs in PowerPoints, dashboards, and emails can...

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Some Applications of Item Response Theory in R

January 11, 2015
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Some Applications of Item Response Theory in R

The typical introduction to item response theory (IRT) positions the technique as a form of curve fitting. We believe that a latent continuous variable is responsible for the observed dichotomous or polytomous responses to a set of items (e.g., multipl...

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