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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
The transcriptional landscape of polyploid wheat
Ricardo H. Ramirez-Gonzalez,Philippa Borrill,Daniel Lang,Sophie A. Harrington,Jemima Brinton,Luca Venturini,Mark W. Davey,John Jacobs,F. van Ex,Asher Pasha,Yogendra Khedikar,Stephen J. Robinson,Aron T. Cory,Tobin Florio,Lorenzo Concia,Caroline Juery,Henk-jan Schoonbeek,Burkhard Steuernagel,Daoquan Xiang,Christopher J. Ridout,Boulos Chalhoub,Klaus F. X. Mayer,Moussa Benhamed,David Latrasse,Abdelhafid Bendahmane,Brande B. H. Wulff,Rudi Appels,Vijay K. Tiwari,Raju Datla,Frédéric Choulet,Curtis J. Pozniak,Nicholas J. Provart,Andrew G. Sharpe,Etienne Paux,Manuel Spannagl,Andrea Bräutigam,Cristobal Uauy +36 more
TL;DR: This study leverages 850 wheat RNA-sequencing samples, alongside the annotated genome, to determine the similarities and differences between homoeolog expression across a range of tissues, developmental stages, and cultivars and suggests that the transposable elements in promoters relate more closely to the variation in the relative expression of homoeologicals across tissues than to a ubiquitous effect across all tissues.
Journal ArticleDOI
Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia
Terrence N. Wong,Giridharan Ramsingh,Andrew L. Young,Christopher A. Miller,Waseem Touma,John S. Welch,Tamara Lamprecht,Dong Shen,Jasreet Hundal,Robert S. Fulton,Sharon Heath,Jack Baty,Jeffery M. Klco,Li Ding,Elaine R. Mardis,Peter Westervelt,John F. DiPersio,Matthew J. Walter,Timothy A. Graubert,Timothy J. Ley,Todd E. Druley,Daniel C. Link,Richard K. Wilson +22 more
TL;DR: The total number of somatic single-nucleotide variants and the percentage of chemotherapy-related transversions are similar in t-AML and de novo AML, indicating that previous chemotherapy does not induce genome-wide DNA damage and suggesting a model in which rare HSPCs carrying age-related TP53 mutations are resistant to chemotherapy and expand preferentially after treatment.
Journal ArticleDOI
Human iPSC-Based Modeling of Late-Onset Disease via Progerin-Induced Aging
Justine D. Miller,Yosif Ganat,Sarah Kishinevsky,Robert L. Bowman,Becky Liu,Edmund Y. Tu,Pankaj Mandal,Pankaj Mandal,Elsa Vera,Jae-Won Shim,Sonja Kriks,Tony Taldone,Noemi Fusaki,Mark J. Tomishima,Dimitri Krainc,Teresa A. Milner,Teresa A. Milner,Derrick J. Rossi,Derrick J. Rossi,Lorenz Studer +19 more
TL;DR: It is suggested that progerin-induced aging can be used to reveal late-onset age-related disease features in hiPSC-based disease models.
Journal ArticleDOI
TOX is a critical regulator of tumour-specific T cell differentiation
Andrew Scott,Andrew Scott,Friederike Dündar,Paul Zumbo,Smita S. Chandran,Christopher A. Klebanoff,Mojdeh Shakiba,Mojdeh Shakiba,Prerak Trivedi,Laura Menocal,Laura Menocal,Heather Appleby,Steven Camara,Dmitriy Zamarin,Tyler Walther,Alexandra Snyder,Matthew R. Femia,Elizabeth A. Comen,Elizabeth A. Comen,Hannah Y Wen,Matthew D. Hellmann,Matthew D. Hellmann,Niroshana Anandasabapathy,Y. Liu,Nasser K. Altorki,Peter Lauer,Olivier Levy,Michael S. Glickman,Michael S. Glickman,Jonathan Kaye,Doron Betel,Mary Philip,Mary Philip,Andrea Schietinger,Andrea Schietinger +34 more
TL;DR: It is hypothesized that the TOX-induced exhaustion program serves to prevent the overstimulation of T cells and activation-induced cell death in settings of chronic antigen stimulation such as cancer.
Journal ArticleDOI
The early spread and epidemic ignition of HIV-1 in human populations
Nuno R. Faria,Andrew Rambaut,Marc A. Suchard,Guy Baele,Trevor Bedford,Melissa J. Ward,Andrew J. Tatem,Joao Sousa,Nimalan Arinaminpathy,Jacques Pépin,David Posada,Martine Peeters,Oliver G. Pybus,Philippe Lemey +13 more
TL;DR: Using statistical approaches applied to HIV-1 sequence data from central Africa, it is shown that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere.