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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
Holocene shifts in the assembly of plant and animal communities implicate human impacts
S. Kathleen Lyons,Kathryn L. Amatangelo,Anna K. Behrensmeyer,Antoine Bercovici,Jessica L. Blois,Matthew A. Davis,Matthew A. Davis,William A. DiMichele,Andrew Du,Jussi T. Eronen,J. Tyler Faith,Gary R. Graves,Gary R. Graves,Nathan A. Jud,Nathan A. Jud,Conrad C. Labandeira,Conrad C. Labandeira,Conrad C. Labandeira,Cindy V. Looy,Brian J. McGill,Joshua H. Miller,David B. Patterson,Silvia Pineda-Munoz,Richard Potts,Brett R. Riddle,Rebecca C. Terry,Anikó B. Tóth,Werner Ulrich,Amelia Villaseñor,Scott L. Wing,Heidi M. Anderson,John M. Anderson,Donald M. Waller,Nicholas J. Gotelli +33 more
TL;DR: Evaluating changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years suggests that the rules governing the assembly of communities have been changed by human activity.
Journal ArticleDOI
Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield.
TL;DR: Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils.
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mdatools – R package for chemometrics
TL;DR: The package was created to give a low entry level for beginners, so they can start using the implemented methods without writing much of code, and users can also have direct access to all computed results thus extending the package functionality by writing own code on top.
Journal ArticleDOI
Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions
Jos R. Wendrich,Bao-Jun Yang,Niels Vandamme,Kevin Verstaen,Wouter Smet,Celien Van de Velde,Max Minne,Brecht Wybouw,Eliana Mor,Helena E. Arents,Jonah Nolf,Julie Van Duyse,Gert Van Isterdael,Steven Maere,Yvan Saeys,Bert De Rybel +15 more
TL;DR: Misexpression of TMO5 and LHW in the entire root meristem was found to increase root hair density, a phenotype resembling wild-type roots grown under phosphate-limiting conditions, and the response of epidermal cells to phosphate deficit was shown to be TMO4-dependent, indicating that the TMO 5-dependent increase in root hairdensity under low-phosphate conditions occurs through a cell nonautonomous effect.
Journal ArticleDOI
Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
TL;DR: It is shown that plasmids can be lost from single-species populations, even when their genes are under selection, because beneficial genes are captured by the chromosome, and that, in a two-species community, between-species transfer maintains community-wide access to plasmid-borne genes, promoting the spread of the ecologically and clinically important genes they carry.