Code and processed data for generating figures in the VIP2B paper

README for VIP2B Figure Folders================================ General Notes-------------Each figure folder contains the data, intermediate results, scripts, or notebooks used to generate the corresponding main or supplementary figure panels. In most cases, the final plotting step is performed using the figure-specific Jupyter notebook provided in that folder.Some analyses require large input files, long-running jobs, or external software. For convenience, several folders already include processed or summarized results that can be used directly for plotting. Use of This Repository----------------------------------1. Figure 1 folder contains nothing but serves as a folder placeholder since Figure 1 is the workflow.2. Use Figure 2 and Figure 3 folders to review benchmarking analyses for taxonomic and functional profiling, respectively.3. Use Figure 4 to examine paired bulk and VLP comparisons.4. Use Figure 5 and Figure 6 folders to explore disease-associated virome features and diversity relationships.5. Use Figure 7 to review disease classification analyses.6. Use Figure 8 to examine virome community type analyses. Important Notes---------------- Some upstream analyses are computationally intensive and may require high-performance computing resources.- Some folders include precomputed results so that figures can be generated without rerunning all upstream analyses.- File paths in the original code may need to be updated if the analyses are rerun on a different system.- This simplified README is intended as a navigation guide. For exact reproducibility, refer to the original figure-specific README files and scripts.See README.txt for more details.VIP2B 图文件夹说明文档 ================================ 通用说明 ------------- 每个图文件夹均包含用于生成对应主图或补充图面板的数据、中间结果、脚本或Jupyter笔记本（Jupyter notebook）。多数情况下，最终绘图步骤通过对应文件夹内提供的专属Jupyter笔记本完成。部分分析需要大型输入文件、长时间运行的任务或外部软件。为方便使用，多个文件夹已包含可直接用于绘图的预处理或汇总结果。 本仓库使用说明 ---------------------------------- 1. 图1文件夹仅作为占位符，因图1为整体工作流程。 2. 分别通过图2、图3文件夹查看分类学与功能谱分析的基准测试分析。 3. 图4文件夹用于探究配对整体样本与病毒样颗粒（VLP）的比较分析。 4. 图5与图6文件夹用于探索疾病相关的病毒组特征与多样性关联关系。 5. 图7文件夹用于查看疾病分类分析。 6. 图8文件夹用于探究病毒组群落类型分析。 重要说明 ---------------- - 部分上游分析计算量较大，需高性能计算资源。 - 部分文件夹已包含预计算结果，可直接生成图表，无需重新运行所有上游分析。 - 若在其他系统中重新运行分析时，需更新原始代码中的文件路径。 - 本简化说明文档仅作为导航指引，如需实现完全可复现的结果，请参考各图专属的说明文件与脚本。 - 更多详情请参阅README.txt。