Data_Sheet_2_Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes.xlsx

Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.

解析基因组结构的复杂性及其独特架构，与用于呈现此类特征的可视化工具的性能水平紧密相关。此类工具需能够提供逼真且可扩展的基因组内容可视化方案。为此，我们推出一款专注于叶绿体（chloroplast）的在线细胞器绘图工具，专为可视化这类基因组的独有结构而开发。该程序的突出独有特性包括：能够以反向互补形式呈现单短拷贝区（Single Short Copy, SSC），借此可描绘每个基因的密码子使用偏好性指数；同时支持处理反向重复区（inverted repeat, IR）与用户自定义绘图图层间的微小错配问题。该程序配备丰富多样的配色方案与功能模块，专为精准且可扩展地呈现质体基因组而设计。我们推出了Shiny应用网站以简化该工具的使用流程；用户还可对官网提供的可下载源代码进行二次开发与修改，以实现更高级的工具应用场景。该软件及其依赖库均采用R语言编写，可通过https://irscope.shinyapps.io/chloroplot/获取。