# 视觉资产与模板来源 / Asset and template sources

| 资产 / Asset | 来源与许可 / Source and license |
| --- | --- |
| `man/figures/logo.png`、`website/assets/logo.webp` | 用户提供的 ggchord 原画，按本项目用途使用，保留作者权利；1254 × 1254 原分辨率，RGBA 逐像素一致。User-provided artwork; author rights retained; full-resolution lossless encodings. |
| `website/assets/favicon.png` | 原画的 64 × 64 显式缩略图；不作为无损原图替代。Explicit thumbnail of the artwork. |
| `man/figures/logo.svg` | 首轮本仓库制作的补充图形，不替代用户原画。Supplementary repository-created design study. |
| 文档数据图 / Documentation plots | 本包及共享 R 代码生成；输入和筛选见 `tools/documentation-examples.R` 与 `website/assets/plots.csv`。Generated by this package; bundled or attributed real inputs and explicit display filters are recorded. |
| pkgdown 模板与脚本 / templates and scripts | [r-lib/pkgdown](https://github.com/r-lib/pkgdown)，[MIT](https://github.com/r-lib/pkgdown/blob/main/LICENSE.md)；生成物保留页脚来源。Footer attribution is retained. |
| Bootstrap | [Bootstrap](https://getbootstrap.com/docs/5.3/about/license/)，MIT；由 bslib/pkgdown 本地复制，保留依赖中的许可头。Copied locally with dependency license notices. |
| jQuery | [jQuery](https://jquery.org/license/)，MIT；由 pkgdown 提供，保留源码许可头。Bundled by pkgdown with its license notice. |
| Font Awesome Free | [Font Awesome Free](https://fontawesome.com/license/free)：图标 CC BY 4.0、字体 SIL OFL 1.1、代码 MIT；由 pkgdown 本地依赖提供，保留许可文件。Icons CC BY 4.0, fonts SIL OFL 1.1, code MIT; dependency notices retained. |

原生模板另带以下浏览器依赖，均保留分发文件中的许可头：

| 依赖 / Dependency | 来源与许可 / Source and license |
| --- | --- |
| Bootstrap TOC | [afeld/bootstrap-toc](https://github.com/afeld/bootstrap-toc)，MIT |
| Headroom.js | [WickyNilliams/headroom.js](https://github.com/WickyNilliams/headroom.js)，MIT |
| clipboard.js | [zenorocha/clipboard.js](https://github.com/zenorocha/clipboard.js)，MIT |
| autocomplete.js | [algolia/autocomplete.js](https://github.com/algolia/autocomplete.js)，MIT；由原生模板分发，不连接托管搜索服务 / Distributed by the template; no hosted search connection |
| Fuse.js | [krisk/Fuse](https://github.com/krisk/Fuse)，本次分发的 v6.4.6 为 Apache-2.0 / Bundled v6.4.6: Apache-2.0 |
| mark.js | [julkue/mark.js](https://github.com/julkue/mark.js)，MIT |

系统正文字体不随仓库分发。网页 CSS/JS 只在原生模板上补充语言切换、代码折叠和本地
搜索和图片查看；不复制参考站文章或图片，数据仅复用下文列明的原始记录。结构参考 gggenomes、ggplot2 等成熟包站的科研
文章阅读方式；调查与配置来源见 `design-roadmap/DOCUMENTATION-REVIEW-v0.16.5.md`。

System text fonts are not redistributed. Custom additions provide language
switching, code disclosure and local search without copying reference-site text
or figures; only attributed source records listed below are reused. The review records the R-package documentation sites used as design references.

本轮新增格式输入来自 gggenomes 公开 EMALE 教程数据归档（MIT，copyright 2018
Thomas Hackl）与 NCBI GenBank L09137.2；没有复用其图片或绘图代码。具体下载 URL、
归档/member/file SHA256、保留的源行号范围及许可说明在
`examples/format-inputs/sources.json`、`README.md` 和 `GGGENOMES-LICENSE.txt` 中。
这些输入随教学输入包提供，生物学身份和原始比对值不为显示而改写。

Added format inputs reuse real EMALE records from the public gggenomes tutorial
archive (MIT; copyright 2018 Thomas Hackl) and NCBI GenBank L09137.2. No upstream
figure or plotting code is reused. Input provenance, physical line ranges and
license notices ship in `examples/format-inputs/` and the tutorial input bundle.

## v0.16.6 旗舰展示与配色 / Flagship figures and colour system

三张showcase图由当前R代码重新生成，未将用户提供的旧版截图或第三方图片作为输出。
弦图和共线性图使用仓库四条FASTA、266条GFF3 CDS及32条原始BLAST HSP；展示
明确筛为12条较长HSP。当前首页不展示GC，相关计算与轨道仍在轨道专题。复杂质粒图
取随包pETDuet-1、常见特征与参考引物，以及commercial_all/unique_6plus酶切子集。

The three showcase images are generated by current R code, not reused user
screenshots or third-party figures. Chord and collinear examples use the four
repository FASTA records, 266 GFF3 CDS and 32 original BLAST HSPs, with an
explicit 12-HSP display subset. The flagship leaves GC to the dedicated track tutorial. The plasmid uses bundled pETDuet-1, curated features,
reference primers and the commercial_all/unique_6plus restriction subset.

序列类别沿用用户参考图的珊瑚红/深蓝灰/青绿/赭黄关系；正负链为红/蓝，相似度为
蓝绿至黄绿的连续标度，背景为暖白。质粒类别保留本包既有紫红编码区、浅绿抗性基因、
黄色起点、蓝色调控与紫色引物。含义不同的类别不强行共用颜色；相同含义保持统一。
共线性的信息层级参考gggenomes、clinker、gggenes官方示例，没有复制它们的绘图代码。

Sequence categories follow the coral/navy/teal/ochre relationship in the supplied
reference. Strands use red/blue, identity uses a blue-green to lime-yellow scale,
and backgrounds are warm white. Plasmid categories retain the package's plum
coding regions, mint resistance genes, yellow origins, blue regulatory features
and purple primers. Shared meanings keep their colours; unrelated categories
are not assigned a misleading common meaning. Collinear composition references
[gggenomes](https://thackl.github.io/gggenomes/),
[clinker](https://github.com/gamcil/clinker) and
[gggenes](https://wilkox.org/gggenes/) without copying their plotting code.

所有展示identity的当前图共享0–100%范围、0/50/80/90/100的颜色位置，以及0/50/80/100的色条刻度，
避免相同相似度随页面的局部数据范围换色。这是文档显式标度，不改变包默认。
All current identity examples share a 0–100% domain, colour positions at
0/50/80/90/100 and readable breaks at 0/50/80/100, so the same identity value
retains its colour across pages.
These are explicit documentation scales; package defaults are unchanged.

当前文档PNG的panel背景透明，plot背景显式统一为 `#FFFCF5`；
截图中的白色feature或标签框仍按其自身语义保留，不做像素替换。
All current documentation PNGs use transparent panel backgrounds over an
explicit `#FFFCF5` plot background; intentional feature and label fills are retained.

本轮补充逐层绘图示例和13个独立质粒参考图。它们均来自当前代码，而不是examples/plasmid中的历史PNG。图库仅在图内适配标签，可隐藏拥挤文字，全部特征几何仍保留。弦图按原始注释顺序四分组抽样并补充负链端部特征，以保留中等密度；方向优化不修改原始链。

Progressive layer examples and13 unique plasmid feature maps are current R outputs, not the historical PNG files in examples/plasmid. Gallery labels fit inside and may hide; feature geometry is retained. Chord features are sampled across annotation order with additional negative-strand endpoints. Orientation optimization changes display only.

GRanges/GInteractions教程结合了[issue #2](https://github.com/DangJem/ggchord/issues/2)的原始需求、当时回复与当前适配器代码；不将仍开放的issue状态当作缺失功能证明，也不将可选依赖跳过计为通过。