The original version of this Article contained a plotting error in Fig. 3g. The Serranidae and Siganidae families were misplaced in the plotted phylogeny. This error has now been corrected in the PDF ...and HTML versions of the Article. For comparison, the original, incorrect version of Fig. 3g is presented below as Fig. 1. The authors thank P. Cowman for identifying the plotting error.
ggtern : Ternary Diagrams Using ggplot2 Hamilton, Nicholas E.; Ferry, Michael
Journal of statistical software,
12/2018, Letnik:
87, Številka:
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This paper presents the ggtern package for R, which has been developed for the rendering of ternary diagrams. Based on the well-established ggplot2 package (Wickham 2009), the present package adopts ...the familiar and convenient programming syntax of its parent. We demonstrate that ggplot2 can be used as the basis for producing specialized plotting packages and, in the present case, a package has been developed specifically for the production of high quality ternary diagrams. In order to produce ggtern, it was necessary to overcome a number of design issues, such as finding a means to modify existing geometries designed for a 2D Cartesian coordinate system and permitting them to function in an environment that requires an additional spatial aesthetic mapping. In the present paper, we provide examples of this package in its most basic form followed by a demonstration of its ease of use, particularly if one is familiar with, and has a predilection towards using ggplot2 on a regular basis.
This work reports the development of low-cost and rapid multiplexed colorimetric assay of antioxidants (total phenolics, antioxidant capacity, flavonoids and anthocyanins) in wines at daisy-shaped ...fluidic paper-based analytical devices (PADs). The desired fluidic patterns were formed on paper by pen drawing and colorimetric reagents were immobilized at the 6 peripheral test zones. The sample was added at the central sample zone, migrated to the test zones and reacted with the immobilized reagents producing characteristic colors that were captured and analyzed. The paper-based approach was applied to the analysis of several wine samples and the results were statistically correlated to standard solution-based colorimetric assays, indicating that it could be reliably used for ranking wines according to their antioxidants content. In addition, the paper-based analytical methodology is simple, instrument-free, portable, cost-effective, rapid and environment friendly.
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•Daisy-shaped paper-based analytical devices (PADs) were fabricated by pen drawing.•The PADs were used for a sextuple antioxidant/phenolics/anthocyanins/flavonoids assay.•Reagents were added to the 6 peripheral test zones and sample was added to the central sample zone.•The results of the assay for 18 wines correlated well with those of solution-based assays (R2 > 0.97).•The paper-based analytical methodology is simple, instrument-free, portable, cost-effective, rapid and environment friendly.
OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python libraries capable ...to generate OncoPrint yet, a big hassle to plot OncoPrints within Python-based genetic variants analysis pipelines. This paper introduces a new Python package PyOncoPrint, which can be easily used to plot OncoPrints in Python. The package is based on the existing widely used scientific plotting library Matplotlib, the resulting plots are easy to be adjusted for various needs.
In this study we introduce linear poly(glycidol) (PG), a structural analog of poly(ethylene glycol) bearing side chains at each repeating unit, as polymer basis for bioink development. We prepare ...allyl- and thiol-functional linear PG that can rapidly be polymerized to a three-dimensionally cross-linked hydrogel network
via
UV mediated thiol-ene click reaction. Influence of polymer concentration and UV irradiation on mechanical properties and swelling behavior was examined. Thiol-functional PG was synthesized in two structural variations, one containing ester groups that are susceptible to hydrolytic cleavage, and the other one ester-free and stable against hydrolysis. This allowed the preparation of degradable and non-degradable hydrogels. Cytocompatibility of the hydrogel was demonstrated by encapsulation of human bone marrow-derived mesenchymal stem cells (hBMSCs). Rheological properties of the hydrogels were adjusted for dispense plotting by addition of high molecular weight hyaluronic acid. The optimized formulation enabled highly reproducible plotting of constructs composed of 20 layers with an overall height of 3.90 mm.
In the last two decades, additive manufacturing (AM) has made significant progress towards the fabrication of biomaterials and tissue engineering constructs. One direction of research is focused on ...the development of mechanically stable implants with patient-specific size/shape and another direction has been to fabricate tissue-engineered scaffolds with designed porous architecture to facilitate vascularization. Among AM techniques, three dimensional powder printing (3DPP) is suitable for fabrication of bone related prosthetic devices, while three dimensional plotting (3DPL) is based on extrusion of biopolymers to create artificial tissues. In the present review, we aim to develop a better understanding of the science and engineering aspects of these low temperature AM techniques (3DPP and 3DPL) in the context of the bone-tissue engineering applications. While recognizing multiple property requirements of a 3D scaffold, the central theme is to discuss the critical roles played by the binder and powder properties together with the interplay among processing parameters in the context of the physics of binder-material interaction for the fabrication of implants with predefined architecture having structural complexity. An effort also has been exerted to discuss the existing challenges to translate the design concepts and material/binder formulations to develop implantable scaffolds with a more emphasis on bioceramics and biopolymers. Summarizing, this review highlights the need to adopt intelligent processing approaches and targeted application-specific biocompatibility characterization, while fabricating mechanically stable and biologically functionalized 3D tissue equivalents.
We produced poro-us poly(ε-caprolactone) (PCL)/hydroxyapatite (HA) composite scaffolds for bone regeneration, which can have a tailored macro/micro-porous structure with high mechanical properties ...and excellent in vitro bioactivity using non-solvent-induced phase separation (NIPS)-based 3D plotting. This innovative 3D plotting technique can create highly microporous PCL/HA composite filaments by inducing unique phase separation in PCL/HA solutions through the non-solvent-solvent exchange phenomenon. The PCL/HA composite scaffolds produced with various HA contents (0 wt %, 10 wt %, 15 wt %, and 20 wt %) showed that PCL/HA composite struts with highly microporous structures were well constructed in a controlled periodic pattern. Similar levels of overall porosity (~78 vol %) and pore size (~248 µm) were observed for all the PCL/HA composite scaffolds, which would be highly beneficial to bone tissue regeneration. Mechanical properties, such as ultimate tensile strength and compressive yield strength, increased with an increase in HA content. In addition, incorporating bioactive HA particles into the PCL polymer led to remarkable enhancements in in vitro apatite-forming ability.
An investigation of what types of extreme wind values are the most suitable for the Gumbel distribution was conducted on Jeju Island, South Korea. Three measurements and reference sites that have ...different topographical conditions were selected to clarify the influence of the topographical conditions on extreme wind values. Because long-term wind data are required to estimate extreme wind speeds with a higher degree of confidence, the MCP (Measure-Correlate-Predict) technique was applied to generate ten-year wind data from one-year measurements. Extreme wind values were sampled from the ten-year wind data based on periodic maximum wind speeds and the wind speeds above a threshold, which were divided into three types each. The six types of extremes were examined to determine which type was more suitable for the Gumbel distribution under the assumption that the Gringorten formula is the best plotting position method for the Gumbel distribution. In addition, we predicted the appropriate wind turbine class for the measurement sites in compliance with IEC international standards. As a result, daily maximum wind speeds were the best extreme wind values for the Gumbel distribution in the six types irrespective of the topographical conditions. The site that has a higher average wind speed was estimated to have a higher extreme wind speed, indicating that a higher wind turbine class was needed at the site.
•We studied on what types of extremes are the most suitable for the Gumbel distribution.•The sites with various topographical conditions were selected to clarify the influence on extremes.•The six types of extremes were sampled from the ten-year wind data.•Daily maximum wind speeds were the best extremes for the Gumbel distribution in the six types.
In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography ...database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information…) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances. Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.
Metagenomics Data Visualization Using R Coleman, Alex; Bose, Anupam; Mitra, Suparna
Methods in molecular biology (Clifton, N.J.),
2023, Letnik:
2649
Journal Article
Communicating key finds is a crucial part of the research process. Data visualization is the field of graphically representing data to help communicate key findings. Building on previous chapters ...around data manipulating using the R programming language this, chapter will explore how to use R to plot data and generate high-quality graphics. It will cover plotting using the base R plotting functionality and introduce the famous ggplot2 package 2 that is widely used for data visualization in R. After this general introduction to data visualization tools, the chapter will explore more specific data visualization techniques for metagenomics data and their use cases using these basic packages.
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