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a linear display", "topics": [ "geom_seq_scale" ] }, { "page": "geom_track_tile", "title": "Draw explicit quantitative tracks along sequence backbones", "topics": [ "geom_track_bar", "geom_track_line", "geom_track_tile" ] }, { "page": "get_chord_layout", "title": "Get the chord layout from a ggchord plot", "topics": [ "get_chord_layout" ] }, { "page": "ggchord", "title": "Layered chord, circular and collinear sequence plots", "topics": [ "ggchord" ] }, { "page": "ggchord_api_contract", "title": "Candidate API and migration contract", "topics": [ "ggchord_api_contract" ] }, { "page": "ggchord_data_contract", "title": "Data workflow and biological coordinate contracts", "topics": [ "ggchord_data_contract" ] }, { "page": "ggchord_layout_contract", "title": "Layout results, units and ownership", "concept": [ "layout results" ], "topics": [ "ggchord_layout_contract" ] }, { "page": "ggplot2-helpers", "title": "Selected ggplot2 helpers for ggchord plots", "topics": [ "aes", "after_scale", "after_stat", "annotate", "element_blank", "element_line", "element_rect", "element_text", "expansion", "ggplot2-helpers", "ggsave", "ggtitle", "guides", "labs", "last_plot", "margin", "PositionIdentity", "position_identity", "rel", "theme", "waiver" ] }, { "page": "grid-helpers", "title": "Physical units and direction arrows", "topics": [ "arrow", "grid-helpers", "unit" ] }, { "page": "guide_ggchord_legend", "title": "Guides for ggchord role aesthetics", "topics": [ "guide_ggchord_colorbar", "guide_ggchord_colourbar", "guide_ggchord_legend" ] }, { "page": "link_ggchord_clusters", "title": "Convert explicit homology-cluster membership to feature links", "topics": [ "link_ggchord_clusters" ] }, { "page": "map_ggchord_position", "title": "Convert genomic positions to or from a linear ggchord layout", "topics": [ "map_ggchord_position" ] }, { "page": "merge_ggchord_ribbons", "title": "Merge adjacent or overlapping alignment blocks of the same sequence pair", "topics": [ "merge_ggchord_ribbons" ] }, { "page": "optimize_ggchord_layout", "title": "Optimize sequence order and orientation for ribbon readability", "topics": [ "optimize_ggchord_layout" ] }, { "page": "plasmid_example_pUC19", "title": "Circular plasmid sequence examples", "topics": [ "plasmid_example_pBluescript_II_SK_plus", "plasmid_example_pBR322", "plasmid_example_pCAMBIA1300", "plasmid_example_pcDNA3_1_plus", "plasmid_example_pDONR221", "plasmid_example_pEarleyGate_201", "plasmid_example_pETDuet_1", "plasmid_example_pET_28a_plus", "plasmid_example_pSB1C3", "plasmid_example_pSpCas9_BB_2A_GFP_PX458", "plasmid_example_pTRE_Tight_BI", "plasmid_example_pTRIPZ", "plasmid_example_pUC19", "plasmid_example_pUC19c" ] }, { "page": "position_feature_stack", "title": "Stack overlapping genes or features on local lanes", "topics": [ "position_feature_stack" ] }, { "page": "position_plasmid", "title": "Place both feature strands on one shared band", "topics": [ "position_plasmid" ] }, { "page": "position_strand", "title": "Place features on opposite sides according to strand", "topics": [ "position_strand" ] }, { "page": "position_track", "title": "Place a quantitative layer in an explicit sequence-local band", "topics": [ "position_track" ] }, { "page": "prepare_ggchord_data", "title": "Prepare named ggchord tables with an explicit audit trail", "topics": [ "prepare_ggchord_data" ] }, { "page": "primer_catalog", "title": "Inspect the bundled sequencing-primer catalogue", "topics": [ "primer_catalog" ] }, { "page": "print.ggchord_clean", "title": "Print a cleaned ggchord data result", "topics": [ "print.ggchord_clean" ] }, { "page": "project_ggchord_features", "title": "Project protein domains or genomic features through a spliced CDS map", "topics": [ "project_ggchord_features" ] }, { "page": "project_ggchord_links", "title": "Project explicitly ungapped protein links to genomic coding segments", "topics": [ "project_ggchord_links" ] }, { "page": "read_bed", "title": "Read BED intervals as ggchord features", "topics": [ "read_bed" ] }, { "page": "read_blast", "title": "Read one or more BLAST tabular output files into ribbon_data format", "topics": [ "read_blast" ] }, { "page": "read_fasta_lengths", "title": "Read one or more FASTA files into seq_data format", "topics": [ "read_fasta_lengths" ] }, { "page": "read_genbank", "title": "Import local GenBank or GBFF records using an optional mature parser", "topics": [ "read_genbank" ] }, { "page": "read_gff3", "title": "Read one or more GFF3 files into gene_data format", "topics": [ "read_gff3" ] }, { "page": "read_paf", "title": "Read PAF mappings as ggchord links", "topics": [ "read_paf" ] }, { "page": "restriction_site_example", "title": "Restriction sites for the minimal single-genome fixture", "topics": [ "restriction_site_example" ] }, { "page": "ribbon_data_example", "title": "Example alignment data", "topics": [ "ribbon_data_example" ] }, { "page": "scale_feature_fill_plasmid", "title": "Plasmid-map feature presets", "topics": [ "scale_feature_fill_plasmid", "scale_feature_shape_plasmid" ] }, { "page": "scale_feature_shape_manual", "title": "Feature shape scale", "topics": [ "scale_feature_shape_manual" ] }, { "page": "scale_gene_fill_manual", "title": "Gene, feature and region fill scales", "topics": [ "scale_feature_fill_manual", "scale_gene_fill_manual", "scale_region_fill_manual" ] }, { "page": "scale_link", "title": "Scales for point links", "topics": [ "scale_link", "scale_link_alpha_continuous", "scale_link_alpha_manual", "scale_link_color_gradientn", "scale_link_color_manual", "scale_link_colour_gradientn", "scale_link_colour_manual", "scale_link_linetype_manual", "scale_link_linewidth_continuous", "scale_link_linewidth_manual" ] }, { "page": "scale_ribbon_alpha_continuous", "title": "Ribbon alpha, outline and linetype scales", "topics": [ "scale_ribbon_alpha_continuous", "scale_ribbon_alpha_manual", "scale_ribbon_color_manual", "scale_ribbon_colour_manual", "scale_ribbon_linetype_manual" ] }, { "page": "scale_ribbon_fill_stepsn", "title": "Ribbon fill scales", "topics": [ "scale_ribbon_fill_gradientn", "scale_ribbon_fill_identity", "scale_ribbon_fill_manual", "scale_ribbon_fill_stepsn" ] }, { "page": "scale_seq_colour_manual", "title": "Sequence colour scales", "topics": [ "scale_seq_color_manual", "scale_seq_colour_manual" ] }, { "page": "scale_seq_position_continuous", "title": "Genomic sequence position scale", "topics": [ "scale_seq_position_continuous" ] }, { "page": "scale_seq_ring_manual", "title": "Explicit sequence ring scale", "topics": [ "scale_seq_ring_manual" ] }, { "page": "scale_track_fill_gradientn", "title": "Set a track's fill or colour mapping", "topics": [ "scale_track_colour_gradientn", "scale_track_colour_manual", "scale_track_fill_gradientn", "scale_track_fill_manual" ] }, { "page": "scale_track_value_continuous", "title": "Set a named track's numerical height scale", "topics": [ "scale_track_value_continuous" ] }, { "page": "segment_ggchord_data", "title": "Prepare independent windows for a segmented linear display", "topics": [ "segment_ggchord_data" ] }, { "page": "seq_data_example", "title": "Example sequence data", "topics": [ "seq_data_example" ] }, { "page": "single_gene_example", "title": "Minimal single-genome gene fixture", "topics": [ "single_gene_example" ] }, { "page": "single_genome_example", "title": "Minimal single-genome sequence fixture", "topics": [ "single_genome_example" ] }, { "page": "stat_ribbon_bundle", "title": "Bundle ribbons as a ggchord stat", "topics": [ "stat_ribbon_bundle" ] }, { "page": "stat_ribbon_density", "title": "Compute local ribbon density as a ggchord stat", "topics": [ "stat_ribbon_density" ] }, { "page": "theme_ggchord", "title": "ggchord themes", "topics": [ "theme_ggchord", "theme_ggchord_dark", "theme_ggchord_minimal", "theme_ggchord_plasmid", "theme_ggchord_publication" ] }, { "page": "validate_ggchord_data", "title": "Validate ggchord input data before plotting", "topics": [ "validate_ggchord_data" ] }, { "page": "validate_ggchord_hierarchy", "title": "Validate explicit genome and contig relationships", "topics": [ "validate_ggchord_hierarchy" ] }, { "page": "view_ggchord", "title": "Preview a ggchord plot at its intended export size", "topics": [ "view_ggchord" ] } ], "_pkglogo": "https://github.com/dangjem/ggchord/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/dangjem/ggchord/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "ggchord_vignette.Rmd", "filename": "ggchord_vignette.html", "title": "ggchord: chord, collinear and plasmid tutorial", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2025-07-07 13:52:01", "modified": "2026-11-02 12:20:23", "commits": 44 }, { "source": "ggchord_guide_hans.Rmd", "filename": "ggchord_guide_hans.html", "title": "ggchord：弦图、共线性图与质粒图教程", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-08-14 06:18:28", "modified": "2026-11-02 12:20:23", "commits": 39 } ], "_score": 6.899273187317604, "_indexed": true, "_nocasepkg": "ggchord", "_universes": [ "dangjem" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.16.6", "date": "2026-11-03T09:57:23.000Z", "distro": "resolute", "commit": "f6e0840cca515a3cabac39ef2bb3dfea5eaf4d11", "fileid": "https://r2.ropensci.org/c0bf6cae7281b49e53669c3720f6087179282771df14caadf97ef4a45f4a6ac6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dangjem/actions/runs/41614328560" }, { "r": "4.6.2", "os": "linux", "version": "0.16.6", "date": "2026-11-03T09:58:06.000Z", "distro": "resolute", "commit": "f6e0840cca515a3cabac39ef2bb3dfea5eaf4d11", "fileid": "https://r2.ropensci.org/31453e09a2e458a0af5099a148a1ff38df7bd1990c3392e7c9dfffad6894e319", "status": "success", 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