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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
Global buffering of temperatures under forest canopies
Pieter De Frenne,Florian Zellweger,Francisco Rodríguez-Sánchez,Brett R. Scheffers,Kristoffer Hylander,Miska Luoto,Mark Vellend,Kris Verheyen,Jonathan Lenoir +8 more
TL;DR: Comparing temperatures in the forest understory versus open habitat across boreal, temperate and tropical biomes, the authors show that tree canopies act as thermal insulators that buffer the understory against temperature extremes.
Journal ArticleDOI
Comparison of the accuracy of human readers versus machine-learning algorithms for pigmented skin lesion classification: an open, web-based, international, diagnostic study.
Philipp Tschandl,Noel C. F. Codella,Bengü Nisa Akay,Giuseppe Argenziano,Ralph P. Braun,Horacio Cabo,David A. Gutman,Allan C. Halpern,Brian Helba,Rainer Hofmann-Wellenhof,Aimilios Lallas,Jan Lapins,Caterina Longo,Josep Malvehy,Josep Malvehy,Michael A. Marchetti,Ashfaq A. Marghoob,Scott W. Menzies,Amanda Oakley,John Paoli,Susana Puig,Susana Puig,Christoph Rinner,Cliff Rosendahl,Alon Scope,Christoph Sinz,H. Peter Soyer,Luc Thomas,Iris Zalaudek,Harald Kittler +29 more
TL;DR: State-of-the-art machine-learning classifiers outperformed human experts in the diagnosis of pigmented skin lesions and should have a more important role in clinical practice.
Journal ArticleDOI
Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota
Soo Ching Lee,Mei San Tang,Yvonne A. L. Lim,Seow Huey Choy,Zachary D. Kurtz,Laura M. Cox,Uma Mahesh Gundra,Ilseung Cho,Richard Bonneau,Martin J. Blaser,Kek Heng Chua,P'ng Loke +11 more
TL;DR: It is suggested that helminth-colonized individuals had greater species richness and number of observed OTUs with enrichment of Paraprevotellaceae, especially with Trichuris infection.
Journal ArticleDOI
Widespread and Functional RNA Circularization in Localized Prostate Cancer
Sujun Chen,Sujun Chen,Sujun Chen,Vincent Huang,Xin Xu,Julie Livingstone,Fraser Soares,Jouhyun Jeon,Yong Zeng,Junjie Tony Hua,Junjie Tony Hua,Jessica Petricca,Jessica Petricca,Haiyang Guo,Miranda Wang,Fouad Yousif,Yuzhe Zhang,Yuzhe Zhang,Yuzhe Zhang,Nilgun Donmez,Musaddeque Ahmed,Stas Volik,Anna Lapuk,Melvin L.K. Chua,Lawrence E. Heisler,Adrien Foucal,Natalie S. Fox,Natalie S. Fox,Michael Fraser,Michael Fraser,Vinayak Bhandari,Vinayak Bhandari,Yu Jia Shiah,Jiansheng Guan,Jiansheng Guan,Jixi Li,Michèle Orain,Valérie Picard,Hélène Hovington,Alain Bergeron,Louis Lacombe,Yves Fradet,Bernard Têtu,Stanley K. Liu,Stanley K. Liu,Felix Y. Feng,Xue Wu,Yang W. Shao,Malgorzata A. Komor,Malgorzata A. Komor,Cenk Sahinalp,Colin Collins,Colin Collins,Youri Hoogstrate,Mark de Jong,Remond J.A. Fijneman,Teng Fei,Guido Jenster,Theodorus van der Kwast,Theodorus van der Kwast,Robert G. Bristow,Paul C. Boutros,Housheng Hansen He,Housheng Hansen He +63 more
TL;DR: Ultra-deep total RNA-seq on 144 tumors with rich clinical annotation revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease.
Journal ArticleDOI
TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues.
Áron Bartha,Balázs Győrffy +1 more
TL;DR: In this article, the authors established an integrated database using available transcriptome-level datasets and created a web platform which enables the mining of this database by comparing normal, tumor and metastatic data across all genes in real time.