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ggplot2: Elegant Graphics for Data Analysis
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TLDR
This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics.Abstract:
This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics. With ggplot2, its easy to: produce handsome, publication-quality plots, with automatic legends created from the plot specification superpose multiple layers (points, lines, maps, tiles, box plots to name a few) from different data sources, with automatically adjusted common scales add customisable smoothers that use the powerful modelling capabilities of R, such as loess, linear models, generalised additive models and robust regression save any ggplot2 plot (or part thereof) for later modification or reuse create custom themes that capture in-house or journal style requirements, and that can easily be applied to multiple plots approach your graph from a visual perspective, thinking about how each component of the data is represented on the final plot. This book will be useful to everyone who has struggled with displaying their data in an informative and attractive way. You will need some basic knowledge of R (i.e. you should be able to get your data into R), but ggplot2 is a mini-language specifically tailored for producing graphics, and youll learn everything you need in the book. After reading this book youll be able to produce graphics customized precisely for your problems,and youll find it easy to get graphics out of your head and on to the screen or page.read more
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Journal ArticleDOI
Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.
Spencer Diamond,Peter F. Andeer,Zhou Li,Alexander Crits-Christoph,David Burstein,David Burstein,Karthik Anantharaman,Karthik Anantharaman,Katherine R Lane,Brian C. Thomas,Chongle Pan,Chongle Pan,Trent R. Northen,Jillian F. Banfield +13 more
TL;DR: Using metagenomics and proteomics on Mediterranean grassland soil samples resulted in the recovery of 793 metagenome-assembled genomes and provided insights into microbial activity in this environment, and how this changes with soil depth and exposure to extended rainfall.
Journal ArticleDOI
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium
David R. Hill,Sha Huang,Melinda S. Nagy,Veda K. Yadagiri,Courtney Fields,Dishari Mukherjee,Brooke Bons,Priya H. Dedhia,Alana M. Chin,Yu Hwai Tsai,Shrikar Thodla,Thomas M. Schmidt,Seth T. Walk,Vincent B. Young,Jason R. Spence +14 more
TL;DR: It is demonstrated that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelio and HIOs are utilized to investigate complex host-microbe interactions in this naive epithelia.
Journal ArticleDOI
Are current atomistic force fields accurate enough to study proteins in crowded environments
Drazen Petrov,Bojan Zagrovic +1 more
TL;DR: In this paper, the authors used explicit-solvent molecular dynamics simulations and a total of 6.4 µs of simulated time to study wild-type and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration.
Journal ArticleDOI
Disentangling the mechanisms shaping the surface ocean microbiota
Ramiro Logares,Ramiro Logares,Ina M. Deutschmann,Pedro C. Junger,Caterina R. Giner,Caterina R. Giner,Anders K. Krabberød,Thomas Schmidt,Laura Rubinat-Ripoll,Mireia Mestre,Mireia Mestre,Mireia Mestre,Guillem Salazar,Guillem Salazar,Clara Ruiz-González,Marta Sebastián,Marta Sebastián,Colomban de Vargas,Silvia G. Acinas,Carlos M. Duarte,Josep M. Gasol,Josep M. Gasol,Ramon Massana +22 more
TL;DR: The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes, suggesting that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration.
Journal ArticleDOI
Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules.
Daniel Mateju,Bastian Th. Eichenberger,Bastian Th. Eichenberger,Franka Voigt,Jan Eglinger,Gregory Roth,Jeffrey A. Chao +6 more
TL;DR: It is demonstrated that mRNA localization to SGs is compatible with translation and argued against a direct role for SGs in inhibition of protein synthesis.