Package: ggchord 0.16.6

Install and prepare the environment | Install and inspect the environment | Which version are you using? | Support evidence | Choose a learning path | Which columns come first? | Optional: check one complete plot | Read the quick result | Optional: save the quick result | Common execution problems | Choose your learning module | Which view should you choose? | Prepare this page | Chord: compare multiple sequences | Collinear: align local comparisons | Circular: annotate one sequence | Check your result | 1.1 Tables and field meanings | Minimal shapes of three tables | Names and optional columns | Inspect real tables | Coordinates and directions | 1.2 Produce and import comparisons | Start with FASTA and GFF3 | Produce your own BLAST results | When another format already exists | 1.3 Build the layers step by step | Prepare this page | Step 1: sequence backbones | Step 2: observed comparisons | Step 3: selected genes | Step 4: label every displayed feature | 1.4 Direction, curvature and clearance | Inspect directional evidence first | Inspect directional evidence | Combine capabilities into a readable view | Why clearance modes look different | Guides and export | 1.5 Filter and summarize links | Prepare this page | Begin with the original link table | Understand each transformation | Density is an explicit statistic | Choose interval ribbons or point links | Check your result | 1.6 Full source-file workflow | Prepare this page | 1. Read and inspect original records | 2. Make the display selection explicit | 3. Build a chord comparison | 4. Inspect all annotations in a linear view | 5. Keep the evidence with the figure | Select fields before passing data | Check your result | Save this result | 1.7 Complete chord showcase | What this view shows | Prepare original records | Compose the layers | Read and adapt the result | Save at its intended size | 2.1 Reuse chord input tables | The same three tables | Obtain the inputs | Current conversion boundaries | 2.2 Switch coordinates and add layers | Prepare this page | Replace coord | Read backbone lengths | Add comparisons | Add strand-separated genes and labels | 2.3 Routes, clearance and the ruler | Prepare this page | Specify controls for long links | Local clearance and dashed outlines | Why the ruler was offset | Continue in depth | 2.4 Compare CDS neighbourhoods | Prepare this page | 1. Extract actual CDS and coding DNA | 2. Declare members and sequence pairs | 3. Focus on comparable neighbourhoods | 4. Project supported protein intervals to both CDS | Check your result | Save this result | 2.5 Focus, anchors and segments | Prepare this page | Focus without losing origins | Independent windows and local reversal | Explicit biological relationships | Map an annotation back to source coordinates | Check your result | 2.6 Complete collinear showcase | Complete result | Prepare original records | Reserve space for connections and labels | Compose the layers | Adjustment and limits | Save at the intended size | 3.1 DNA, annotations and 13 references | Tables and optional information | Inspect bundled real records | Import your own plasmid | A progressive case sequence | 3.2 From a circle to annotation layers | Prepare this page | Step 1: double backbone and centre name | Step 2: feature shapes | Step 3: fitted feature labels | Step 4: primers and selected restriction sites | 3.3 Features, primers and restriction | Prepare this page | Search and display are separate | Restriction interpretation | General feature recognition | Follow an annotated reference workflow | Check your result | 3.4 Thirteen plasmid references | Prepare all cases once | Inputs and recognition results | pSB1C3: Small vector and basic structure | pUC19: Common features and replication origin | pBR322: Multiple resistance regions and direction | pBluescript II SK(+): Local regulation and short features | pET-28a(+): Expression regions and tags | pETDuet-1: Dual expression units; transition to the dense case | pDONR221: Recombination-related architecture | pcDNA3.1(+): Annotation hierarchy in an expression vector | pTRE-Tight-BI: Bidirectional regulatory structure | pTRIPZ: Display density on a longer sequence | pCAMBIA1300: Architecture of a larger plant vector | pEarleyGate 201: Category comparison with another plant vector | pSpCas9(BB)-2A-GFP (PX458): Large expression vector and label fitting | Next | 3.5 Complete plasmid cases | Prepare this page | Use a source-backed sequence | Compose independent layers | Read the annotation layers | Choose the displayed sites deliberately | Understand catalogue and label limits | Adapt the workflow | Check your result | Save this result | Complete example: a dense pETDuet-1 map | Prepare tables and coordinates | Prepare this page | Tables | Coordinate contract | Import original records | Validate, clean, prepare | Inspect a problematic input and its repair report | Declare genome and contig keys | Minimal input and protein alignments | Check your result | Import and convert data | Prepare this page | Adapt an existing table | BED and PAF: convert coordinates once | GenBank: retain record identity | Optional interval objects | Check your result | Import nucleotide and protein alignments | Prepare this page | Use the default tabular columns | File layout and minimal plotting fields differ | Read BLASTp with explicit coordinate units | Sources and limits | Check your result | Project protein intervals to genomic coordinates | Prepare this page | Start with source-backed CDS | Segments, phase and partial regions | BLASTp query spans and two-ended links | Check your result | Features, stacking and genomic decoration | Prepare this page | Preserve feature semantics | Choose shapes by meaning | Highlight an interval without rewriting observations | Check your result | Labels and local placement | Prepare this page | Select a layout | Fixed and automatic placement | Match anchors across layers | Compare the three gene layouts | Check your result | Quantitative tracks | Prepare this page | Compute a track from actual DNA | Draw GC fractions | Share an ID deliberately | Inspect retention and limits | Combine bars, a moving mean and annotation bands | Check your result | Save this result | Mappings, scales, guides and themes | Prepare this page | Build styles from data roles | Fixed styles and user scale priority | Make legends readable | Select a theme for the scene | Check your result | Set values by sequence and strand | Prepare this page | The capability remains supported | Supported parameters | Compatibility and design tradeoffs | Check your result | Common adjustments and grammar | Prepare this page | Assign each responsibility | Map link identity | Place features | Check your result | Export, preview and diagnostics | Prepare this page | Save the intended size | Consume geometry by name | Interpret evidence | Complete layout, tables and opt-in ordering | Check your result | Articles and complete workflows | Three learning paths | Read in order or consult as needed | Setup and learning paths | Module I · Chord | Module II · Collinear | Module III · Plasmid | Consult as needed · Data and layers | Learning map and reference | Capabilities and runnable evidence | Reproducible gallery | Find a figure by task | Figures and dimensions | One source for both languages | Reproduce | Asset sources | Frequently asked questions | Why are labels different after resizing? | Why did an old parameter stop working? | Why is a feature rejected as a gene? | Why is a ribbon missing in linear mode? | Can the package compute alignments or validate primer experiments? | Is a measured diagnostic a release certification? | Where should I report a problem? | Migrate to the candidate API | Scope and timing | Replacement table | Run the replacement | What remains supported | Terminology and design sources | Shared terminology | Design and asset provenance

安装与环境准备 | 安装并确认环境 | 你正在使用哪个版本？ | 支持证据 | 选择一条学习路线 | 输入表先看哪些列？ | 可选：快速确认一次绘图 | 如何阅读这个快速结果 | 可选：保存快速结果 | 常见运行问题 | 选择合适的学习模块 | 怎么选择？ | 本页准备 | 弦图：比较多条序列 | 共线性图：对齐局部比较 | 圆图：注释单条序列 | 完成后检查 | 1.1 输入表与字段含义 | 三张表的最小形状 | 名称与可选列 | 查看真实表格 | 坐标与方向 | 1.2 生成与导入比对数据 | 从FASTA与GFF3开始 | 用BLAST产生自己的结果 | 已有其他格式时 | 1.3 从骨架逐层添加 | 本页准备 | 第一步：只有序列骨架 | 第二步：加入已有比对 | 第三步：加入精选基因 | 第四步：给每个展示特征加标签 | 1.4 方向、曲率与避障 | 本页准备 | 先检查方向证据 | 将功能组合成可读的图 | 避障方式为何看起来不同 | 颜色与导出 | 1.5 筛选与整理连接 | 本页准备 | 从原始连接表开始 | 理解每步转换 | 密度是显式统计 | 选择区间区间连接或点连接 | 完成后检查 | 1.6 原始文件完整流程 | 本页准备 | 1. 读取并检查原始记录 | 2. 明确显示筛选规则 | 3. 构建弦图比较 | 4. 在线性视图检查全部注释 | 5. 随图保留证据 | 先选列，再传入函数 | 完成后检查 | 保存本页结果 | 1.7 弦图综合展示 | 综合结果 | 准备原始记录 | 组合图层 | 阅读与调整 | 按预定尺寸保存 | 2.1 复用弦图的数据 | 相同的三张表 | 数据如何获得 | 当前转换边界 | 2.2 只替换坐标系，再逐层添加 | 本页准备 | 替换coord | 从骨架看比例 | 加入连接 | 加入上下分链与标签 | 2.3 跨行连接、避障与比例尺 | 本页准备 | 明确长连接的控制点 | 局部缺口与虚线 | 比例尺为何曾经没对齐 | 继续深入 | 2.4 比较基因邻域 | 本页准备 | 1. 提取实际 CDS 与编码 DNA | 2. 显式声明成员和序列对 | 3. 聚焦到可比较的邻域 | 4. 将有证据的蛋白区间投影到两端 CDS | 完成后检查 | 保存本页结果 | 2.5 局部、锚定与分段 | 本页准备 | 保留来源的局部聚焦 | 独立窗口与局部翻转 | 显式生物学关系 | 按源坐标放置普通注释 | 完成后检查 | 2.6 共线性综合展示 | 综合结果 | 准备原始记录 | 为连接和标签保留空间 | 组合图层 | 调整与限制 | 按预定尺寸保存 | 3.1 DNA、注释与13个参考序列 | 输入表与可选信息 | 查看随包真实记录 | 导入自己的质粒 | 案例如何循序渐进 | 3.2 从圆圈到多层注释 | 本页准备 | 第一步：双线骨架与中心名称 | 第二步：加入特征形状 | 第三步：为特征适配标签 | 第四步：引物与选定酶切位点 | 3.3 识别特征、引物与酶切 | 本页准备 | 搜索与显示分开 | 解释酶切结果 | 通用注释识别 | 跟随完整参考注释流程 | 完成后检查 | 3.4 13个质粒参考案例 | 一次准备全部案例 | 输入与识别结果 | pSB1C3：小载体与基本骨架 | pUC19：常见注释与复制起点 | pBR322：多个抗性区与方向 | pBluescript II SK(+)：局部调控与短特征 | pET-28a(+)：表达区与标签 | pETDuet-1：双表达单元，进入密集案例 | pDONR221：重组相关结构 | pcDNA3.1(+)：表达载体的注释层级 | pTRE-Tight-BI：双向调控布局 | pTRIPZ：更长序列的显示密度 | pCAMBIA1300：较大植物载体的结构 | pEarleyGate 201：另一植物载体的类别对照 | pSpCas9(BB)-2A-GFP (PX458)：大型表达载体与文字适配 | 下一步 | 3.5 质粒综合实战 | 本页准备 | 使用有来源的序列 | 组合独立图层 | 阅读各注释层 | 有意选择显示位点 | 理解目录和标签的限制 | 应用到自己的数据 | 完成后检查 | 保存本页结果 | 完整示例：pETDuet-1 密集质粒图 | 数据与坐标 | 本页准备 | 输入表 | 坐标契约 | 导入原始记录 | 校验、清理与准备 | 检查问题输入及修复报告 | 声明 genome 与 contig 键 | 最小输入与蛋白比对 | 完成后检查 | 导入和转换数据 | 本页准备 | 把已有表格转换成需要的列 | BED 和 PAF：坐标只转换一次 | GenBank：保留记录身份 | 可选的区间对象 | 完成后检查 | 导入核酸和蛋白比对 | 本页准备 | 默认表格列就够用 | 文件布局与绘图最小列是两回事 | BLASTp 可以读取，但坐标单位不同 | 来源与限制 | 完成后检查 | 将蛋白区间转换为基因组坐标 | 本页准备 | 先准备有来源的 CDS | 分段、phase 和部分区域 | BLASTp 查询范围与双端连接 | 完成后检查 | 绘制注释与处理重叠 | 本页准备 | 保留注释语义 | 按含义选择形状 | 高亮区间而不改写观测 | 完成后检查 | 放置和调整标签 | 本页准备 | 选择布局 | 固定与自动放置 | 跨层匹配锚点 | 对照三种基因标签布局 | 完成后检查 | 添加数据轨道 | 本页准备 | 从实际 DNA 计算数据轨道 | 绘制 GC 比例 | 同一 ID 共享同一条轨道 | 检查裁剪和数值范围 | 叠加柱、滑动均值和注释带 | 完成后检查 | 保存本页结果 | 设置配色、图例和主题 | 本页准备 | 从数据角色构建样式 | 固定样式和用户标度优先 | 组织可读图例 | 为场景选择主题 | 完成后检查 | 按序列和链设置参数 | 本页准备 | 这个能力仍然保留 | 哪些参数支持 | 兼容写法与取舍 | 完成后检查 | 调整图形 | 本页准备 | 职责分配 | 映射连接相似度 | 放置注释 | 完成后检查 | 预览和保存图形 | 本页准备 | 按目标尺寸保存 | 按字段名消费几何 | 理解诊断证据 | 完整布局、表格与主动选择的排序 | 完成后检查 | 使用教程 | 三条学习路线 | 依次阅读或按需查阅 | 安装与学习路线 | 模块一『弦图』部分 | 模块二『共线性图』部分 | 模块三『质粒图』部分 | 按需查阅：数据与图层 | 学习地图与函数查阅 | 功能与可运行证据 | 示例图集 | 按任务找图 | 图片与尺寸 | 两种语言共用一个来源 | 重建 | 资产来源 | 常见问题 | 调整尺寸后标签为什么不同？ | 旧参数为什么报错？ | 注释为什么不能作为 gene 绘制？ | 直线模式的区间连接为什么没显示？ | 包会计算比对或验证引物实验吗？ | 已测量诊断等于发布认证吗？ | 在哪里报告问题？ | 迁移到候选 API | 范围与时间 | 替代表 | 运行当前替代 | 保留的支持 | 术语说明 | 对照术语 | 设计与资产来源