Extending ggplot2 for Linked and Animated Web Graphics

Sievert, Carson; VanderPlas, Susan; Cai, Jun; Ferris, Kevin; Khan, Faizan; Hocking, Toby Dylan

doi:10.1080/10618600.2018.1513367

Cited by 5 publications

(3 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Distance-decay relationship (DDR) analysis used the geosphere package ( 33 ). Canonical correspondence analysis (CCA) based on Bray–Curtis distance was visualized with the ggplot2 package ( 34 ) and the ANOVA test was carried out with the permutest function ( 35 ). The envfit function was used to test the correlation between each environmental factor and gut community ( 36 ).…”

Section: Methodsmentioning

confidence: 99%

Gut microbiome diversity and biogeography for Chinese bumblebee Bombus pyrosoma

Zhang,

Guo,

Zhuang

et al. 2024

mSystems

View full text Add to dashboard Cite

Gut microbiota of the bumblebee is critical as it modulates the health and fitness of the host. However, the mechanisms underlying the formation and maintenance of the diversity of bumblebee gut bacteria over a long period of evolution have yet to be elucidated. In particular, the gut bacterial diversity and community assembly processes of Bombus pyrosoma across the Chinese border remain unclear. In this study, we systematically carried out unprecedented sampling of 513 workers of the species Bombus pyrosoma across the Chinese landscape and used full-length 16S rRNA gene sequencing to examine their gut microbiota diversity and biogeography. The gut microbiota composition and community structure of Bombus pyrosoma from different geographical locations were diverse. On the whole, the gut bacteria Gilliamella and Snodgrassella are dominant in bumblebees, but opportunistic pathogens Serratia and Pseudomonas are dominant in some sampling sites such as Hb15, Gs1, Gs45, Qhs15, and Ssx35. All or part of environmental factors such as latitude, annual mean temperature, elevation, human footprint, population density, and annual precipitation can affect the alpha diversity and community structure of gut bacteria. Further analysis showed that the assembly and shift of bumblebee gut bacterial communities under geographical variation were mainly driven by the stochastic drift of the neutral process rather than by variable selection of niche differentiation. In conclusion, our unprecedented sampling uncovers bumblebee gut microbiome diversity and shifts over evolutionary time. IMPORTANCE The microbiotas associated with organisms facilitates host health and fitness, and the homeostasis status of gut microbiota also reflects the habitat security faced by the host. In addition, managing gut microbiota is important to improve bumblebee health by understanding the ecological process of the gut microbiome. Thus, we first carried out an runprecedented sampling of 513 workers of the species Bombus pyrosoma across the Chinese landscape and used full-length 16S rRNA gene sequencing to uncover their gut microbiota diversity and biogeography. Our study provides new insights into the understanding of gut microbiome diversity and shifts for Chinese Bumblebee over evolutionary time.

show abstract

Section: Methodsmentioning

confidence: 99%

Gut microbiome diversity and biogeography for Chinese bumblebee Bombus pyrosoma

Zhang,

Guo,

Zhuang

et al. 2024

mSystems

View full text Add to dashboard Cite

show abstract

“…The interactivity is made possible by Vega ( Satyanarayan et al, 2016 ) for rendering graphics on a web browser. The animint2 R package layers interactivity directly on a ggplot2 plot by translating the plot into JavaScript with a set of standard interactions ( Sievert et al, 2019 ). The cranvas package documented by Xie et al, (2014) illustrates how a scriptable interactive data visualization system might be engineered in R with an appropriate toolkit.…”

Section: Interactive Graphicsmentioning

confidence: 99%

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1

Morota

Cheng

Cook

et al. 2021

Journal of Animal Science

View full text Add to dashboard Cite

Statistical graphics, and data visualization, play an essential but under-utilized, role for data analysis in animal science, and also to visually illustrate the concepts, ideas, or outputs of research and in curricula. The recent rise in web technologies and ubiquitous availability of web browsers enables easier sharing of interactive and dynamic graphics. Interactivity and dynamic feedback enhance human–computer interaction and data exploration. Web applications such as decision support systems coupled with multimedia tools synergize with interactive and dynamic graphics. However, the importance of graphics for effectively communicating data, understanding data uncertainty, and the state of the field of interactive and dynamic graphics is underappreciated in animal science. To address this gap, we describe the current state of graphical methodology and technology that might be more broadly adopted. This includes an explanation of a conceptual framework for effective graphics construction. The ideas and technology are illustrated using publicly available animal datasets. We foresee that many new types of big and complex data being generated in precision livestock farming create exciting opportunities for applying interactive and dynamic graphics to improve data analysis and make data-supported decisions.

show abstract

“…Examples from biology include metabolic maps (Noronha et al 2017), genome assemblies (Wick et al 2015), scRNA-Seq data (Hillje et al 2020), QTL data (Broman 2015) and many more. While such solutions are each tailored for one very specific type of data, there are also a number of general low-level frameworks to create interactive apps, such as D3 (Bostock et al 2011) and Vega-Lite (Satyanarayan et al 2015), and more highlevel but still general-purpose packages, such as Vega (Satyanarayan et al 2016), Shiny (RStudio, Inc 2013), BPG (P’ng et al 2019), and plotly (Sievert et al 2019; Sievert 2020). However, the gap between these generalpurpose frameworks and special-purpose apps is still wide, as we discuss below.…”

Section: Introductionmentioning

confidence: 99%

R/LinkedCharts: A novel approach for simple but powerful interactive data analysis

Ovchinnikova

Anders

2022

Preprint

View full text Add to dashboard Cite

In any research project involving data-rich assays, exploratory data analysis is a crucial step. Typically, this involves jumping back and forth between visualizations that provide overview of the whole data and others that dive into details. In data quality assessment, for example, it might be very helpful to have one chart showing a summary statistic for all samples, and clicking on one of the data points would display details on this sample in a second plot. Setting up such interactively linked charts is usually too cumbersome and time-consuming to use them in ad hoc analysis. We present R/LinkedCharts, a framework that renders this task radically simple: Producing linked charts is as quickly done as is producing conventional static plots in R, requiring a data scientist to write only very few lines of simple R code to obtain complex and general visualization. We expect that the convenience of our new tool will enable data scientists and bioinformaticians to perform much deeper and more thorough EDA with much less effort. Furthermore, R/LinkedCharts apps, typically first written as quick-and-dirty hacks, can also later be polished to provide interactive data access in publication quality, thus contributing to open science.

show abstract

Extending ggplot2 for Linked and Animated Web Graphics

Cited by 5 publications

References 17 publications

Gut microbiome diversity and biogeography for Chinese bumblebee Bombus pyrosoma

Gut microbiome diversity and biogeography for Chinese bumblebee Bombus pyrosoma

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1

R/LinkedCharts: A novel approach for simple but powerful interactive data analysis

Contact Info

Product

Resources

About