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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
A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus.
TL;DR: This work provides detailed characterization of a TF gene cluster and advances the understanding of the transcriptional and post-translational regulatory mechanisms that govern TIA biosynthesis in C. roseus.
Journal ArticleDOI
Gene flow contributes to diversification of the major fungal pathogen Candida albicans.
Jeanne Ropars,Jeanne Ropars,Corinne Maufrais,Dorothée Diogo,Marina Marcet-Houben,Marina Marcet-Houben,Aurélie Perin,Natacha Sertour,Kevin Mosca,Emmanuelle Permal,Guillaume Laval,Christiane Bouchier,Laurence Ma,Katja Schwartz,Kerstin Voelz,Robin C. May,Julie Poulain,Julie Poulain,Christophe Battail,Patrick Wincker,Patrick Wincker,Andrew M. Borman,Anuradha Chowdhary,Shangrong Fan,Soo Hyun Kim,Patrice Le Pape,Orazio Romeo,Jong Hee Shin,Toni Gabaldón,Gavin Sherlock,Marie-Elisabeth Bougnoux,Marie-Elisabeth Bougnoux,Marie-Elisabeth Bougnoux,Christophe d'Enfert +33 more
TL;DR: Evidence of gene flow between previously known and newly identified genetic clusters is found, supporting the occurrence of parasexuality in nature and thus C. albicans takes advantage of both clonality and gene flow to diversify.
Journal ArticleDOI
Ancient goat genomes reveal mosaic domestication in the Fertile Crescent
Kevin G. Daly,Pierpaolo Maisano Delser,Pierpaolo Maisano Delser,Victoria E. Mullin,Victoria E. Mullin,Amelie Scheu,Amelie Scheu,Valeria Mattiangeli,Matthew D. Teasdale,Matthew D. Teasdale,Andrew J. Hare,Joachim Burger,Marta Pereira Verdugo,Matthew J. Collins,Matthew J. Collins,Ron Kehati,Cevdet Merih Erek,Guy Bar-Oz,François Pompanon,Tristan Cumer,Canan Çakirlar,Azadeh Fatemeh Mohaseb,Azadeh Fatemeh Mohaseb,Delphine Decruyenaere,Hossein Davoudi,Özlem Çevik,Gary O. Rollefson,Jean-Denis Vigne,Roya Khazaeli,Homa Fathi,Sanaz Beizaee Doost,Roghayeh Rahimi Sorkhani,Ali A. Vahdati,Eberhard Sauer,Hossein Azizi Kharanaghi,Sepideh Maziar,Boris Gasparian,Ron Pinhasi,Louise Martin,David Orton,Benjamin S. Arbuckle,Norbert Benecke,Andrea Manica,Liora Kolska Horwitz,Marjan Mashkour,Marjan Mashkour,Daniel G. Bradley +46 more
TL;DR: It is demonstrated that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region.
Journal ArticleDOI
Deciphering Pancreatic Islet β Cell and α Cell Maturation Pathways and Characteristic Features at the Single-Cell Level
TL;DR: It is discovered that β and α cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times, and insights are provided into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both β andα cells.
Journal ArticleDOI
T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.
Asaf Madi,Asaf Poran,Eric Shifrut,Shlomit Reich-Zeliger,Erez Greenstein,Irena Zaretsky,Tomer Arnon,Tomer Arnon,François Van Laethem,Alfred Singer,Jinghua Lu,Peter D. Sun,Irun R. Cohen,Nir Friedman +13 more
TL;DR: This paper found that abundant CDR3-TCRβ sequences were clustered within networks generated by sequence similarity, suggesting that the immune system distributes its TCR sequences unevenly, attending to specific foci of reactivity.