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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 pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy
Matthias C. Munder,Daniel Midtvedt,Titus M. Franzmann,Elisabeth Nüske,Oliver Otto,Maik Herbig,Elke Ulbricht,Paul Müller,Anna Taubenberger,Shovamayee Maharana,Liliana Malinovska,Doris Richter,Jochen Guck,Vasily Zaburdaev,Simon Alberti +14 more
TL;DR: Dormancy in different eukaryotic organisms is found to be associated with a significant decrease in the mobility of organelles and foreign tracer particles, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability.
Journal ArticleDOI
TREM2 Regulates Microglial Cholesterol Metabolism upon Chronic Phagocytic Challenge.
Alicia A. Nugent,Karin Lin,Bettina Van Lengerich,Steve Lianoglou,Laralynne Przybyla,Sonnet S. Davis,Ceyda Llapashtica,Junhua Wang,Do Jin Kim,Dan Xia,Anthony Lucas,Sulochanadevi Baskaran,Patrick C.G. Haddick,Melina Lenser,Timothy K. Earr,Ju Shi,Jason C. Dugas,Benjamin J. Andreone,Todd P. Logan,Hilda Solanoy,Hang Chen,Ankita Srivastava,Suresh Poda,Pascal E. Sanchez,Ryan J. Watts,Thomas Sandmann,Giuseppe Astarita,Joseph W. Lewcock,Kathryn M. Monroe,Gilbert Di Paolo +29 more
TL;DR: Combining chronic demyelination paradigms and cell sorting with RNA sequencing and lipidomics, it is found that wild-type microglia acquire a disease-associated transcriptional state, while TREM2-deficientmicroglia remain largely homeostatic, leading to neuronal damage.
Journal ArticleDOI
Clustering trees: a visualization for evaluating clusterings at multiple resolutions
Luke Zappia,Alicia Oshlack +1 more
TL;DR: This visualization shows the relationships between clusters at multiple resolutions, allowing researchers to see how samples move as the number of clusters increases, and to explore and examine the impact of varying clustering resolution.
Journal ArticleDOI
Exploiting rRNA operon copy number to investigate bacterial reproductive strategies.
TL;DR: The findings imply that basic cellular processes adapt in contrasting ways to long-term differences in resource availability, and establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements.