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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
Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.
Bela Hausmann,Bela Hausmann,Klaus-Holger Knorr,Katharina Schreck,Susannah G. Tringe,Tijana Glavina del Rio,Alexander Loy,Michael Pester,Michael Pester +8 more
TL;DR: It is shown that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.
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Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies.
Jonathan Thorsen,Asker Daniel Brejnrod,Martin S. Mortensen,Morten Arendt Rasmussen,Jakob Stokholm,Waleed Abu Al-Soud,Søren J. Sørensen,Hans Bisgaard,Johannes Waage +8 more
TL;DR: The robustness of available methods for inference in differential relative abundance analysis and beta-diversity-based sample separation is assessed using a rigorous benchmarking framework based on large clinical 16S microbiome datasets from different sources, providing an easily extensible framework for benchmarking of new methods and future microbiome datasets.
Journal ArticleDOI
A new species of Homo from the Late Pleistocene of the Philippines
Florent Détroit,Armand Salvador B. Mijares,Julien Corny,Guillaume Daver,Clément Zanolli,Eusebio Z. Dizon,Emil Charles Robles,Rainer Grün,Philip Piper,Philip Piper +9 more
TL;DR: Homo luzonensis is a new species of Homo from the Callao Cave in the Philippines from the Late Pleistocene epoch that displays a combination of primitive and derived morphological features that is different from the combination of features found in other species in the genus Homo.
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The citation advantage of linking publications to research data
Giovanni Colavizza,Giovanni Colavizza,Iain Hrynaszkiewicz,Iain Hrynaszkiewicz,Isla Staden,Isla Staden,Kirstie Whitaker,Kirstie Whitaker,Barbara McGillivray,Barbara McGillivray +9 more
TL;DR: In this paper, the authors consider 531, 889 journal articles published by PLOS and BMC and develop an automatic system for labelling their data availability statements according to four categories based on their content and the type of data availability they display, and analyze the citation advantage of different statement categories via regression.
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Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity.
Daisy A. Hoagland,Rasmus Møller,Skyler Uhl,Kohei Oishi,Justin J. Frere,Ilona Golynker,Shu Horiuchi,Maryline Panis,Daniel Blanco-Melo,David H. Sachs,Knarik Arkun,Jean K. Lim,Benjamin R. tenOever +12 more
TL;DR: In this paper, the authors investigated the dynamics of the systemic response to SARS-CoV-2 in hamsters by histological analysis and transcriptional profiling, and they found that the antiviral response with intranasal administration of recombinant IFN-I reduced viral disease, prevented transmission, and lowered inflammation in vivo.