shinyCircos‐V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features

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Abstract

We previously developed shinyCircos, an interactive web application for creating Circos diagrams, which has been widely recognized for its graphical user interface and ease of use. Here, we introduce shinyCircos‐V2.0, an upgraded version of shinyCircos that includes a new user interface with enhanced usability and many new features for creating advanced Circos plots. To help users get started with shinyCircos‐V2.0, we provide detailed tutorials and example input data sets. The application is available online at https://venyao.xyz/shinyCircos/ and https://asiawang.shinyapps.io/shinyCircos/, or can be installed locally using the source code deposited in GitHub ( https://github.com/YaoLab-Bioinfo/shinyCircos-V2.0).

Abstract

We developed a web application called shinyCircos‐V2.0 for creating Circos plots. The process of creating a Circos plot with shinyCircos‐V2.0 involves three simple steps: uploading the input data, setting the plotting parameters, and generating the Circos plot. Our application offers a wide range of plotting parameters that can be used to enhance the appearance of the resulting Circos plot. Overall, shinyCircos‐V2.0 simplifies the creation of Circos plots and provides researchers with a powerful tool for data visualization.

Highlights

We presented a web application shinyCircos‐V2.0 for creation of a Circos plot.
shinyCircos‐V2.0 is an upgraded version of shinyCircos with a more user‐friendly interface and many new features.
Detailed tutorials and example input data sets are provided to enhance the usability of shinyCircos‐V2.0.

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Most cited references 14

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Circos: an information aesthetic for comparative genomics.

Martin Krzywinski, Jacqueline Schein, Inanç Birol … (2009)

We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

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circlize Implements and enhances circular visualization in R.

Zuguang Gu, Lei Gu, Roland Eils … (2014)

Circular layout is an efficient way for the visualization of huge amounts of genomic information. Here we present the circlize package, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding genomic patterns behind multi-dimensional data.

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Is Open Access

Complex heatmap visualization

Zuguang Gu (2022)

Heatmap is a widely used statistical visualization method on matrix‐like data to reveal similar patterns shared by subsets of rows and columns. In the R programming language, there are many packages that make heatmaps. Among them, the ComplexHeatmap package provides the richest toolset for constructing highly customizable heatmaps. ComplexHeatmap can easily establish connections between multisource information by automatically concatenating and adjusting a list of heatmaps as well as complex annotations, which makes it widely applied in data analysis in many fields, especially in bioinformatics, to find hidden structures in the data. In this article, we give a comprehensive introduction to the current state of ComplexHeatmap , including its modular design, its rich functionalities, and its broad applications. Complex heatmap is a powerful visualization method for revealing associations between multiple sources of information. We have developed an R package named ComplexHeatmap that provides comprehensive functionalities for heatmap visualization. It has been widely used in the bioinformatics community. We give a comprehensive introduction to the current state of ComplexHeatmap in this article. Complex heatmap is a powerful visualization method for revealing associations between multiple sources of information. We have developed an R package named ComplexHeatmap that provides comprehensive functionalities for heatmap visualization. It has been widely used in the bioinformatics community. We give a comprehensive introduction to the current state of ComplexHeatmap in this article.

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Author and article information

Contributors

Wen Yao:

ORCID: http://orcid.org/0000-0002-0643-506X

yaowen@henau.edu.cn

Journal

Journal ID (nlm-ta): Imeta

Journal ID (iso-abbrev): Imeta

Journal ID (doi): 10.1002/(ISSN)2770-596X

Journal ID (publisher-id): IMT2

Title: iMeta

Publisher: John Wiley and Sons Inc. (Hoboken )

ISSN (Print): 2770-5986

ISSN (Electronic): 2770-596X

Publication date (Electronic): 08 May 2023

Publication date Collection: May 2023

Volume: 2

Issue: 2 ( doiID: 10.1002/imt2.v2.2 )

Electronic Location Identifier: e109

Affiliations

[ ¹ ] National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences Henan Agricultural University Zhengzhou China

[ ² ] Henan Institute of Crop Molecular Breeding Henan Academy of Agricultural Sciences Zhengzhou China

[ ³ ] College of Agriculture Henan University Kaifeng China

Author notes

[*] [* ] Correspondence Wen Yao, National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China.

Email: yaowen@ 123456henau.edu.cn

Author information

Wen Yao http://orcid.org/0000-0002-0643-506X

Article

Publisher ID: IMT2109

DOI: 10.1002/imt2.109

PMC ID: 10989951

PubMed ID: 38868422

SO-VID: 2bdff98d-6274-4be4-b8a2-e6b927e6afdb

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

History

Date revision received : 01 April 2023

Date received : 23 February 2023

Date accepted : 13 April 2023

Page count

Figures: 5, Tables: 0, Pages: 9, Words: 3931

Funding

Funded by: Scientific and Technological Research Project of Henan Province

Award ID: 212102110243

Funded by: National Natural Science Foundation of China , doi 10.13039/501100001809;

Award ID: 32101745

Funded by: Research start‐up fund to topnotch talents of Henan Agricultural University

Award ID: 30500581

Funded by: Natural Science Foundation of Henan Province , doi 10.13039/501100006407;

Award ID: 232300420011

Custom metadata

source-schema-version-number 2.0

cover-date May 2023

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.0 mode:remove_FC converted:25.03.2024

Keywords: circos,data visualization,r/shiny,shinycircos,web application

Data availability:

Keywords: circos, data visualization, r/shiny, shinycircos, web application

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shinyCircos‐V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features

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Most cited references 14

Circos: an information aesthetic for comparative genomics.

circlize Implements and enhances circular visualization in R.

Complex heatmap visualization

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