本页完整说明已译为现代汉语;函数、参数、代码和原始数据标识保留原样。 使用教程
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安装与学习路线
首页安装与环境准备选择合适的学习模块模块一『弦图』部分
1.1 输入表与字段含义1.2 生成与导入比对数据1.3 从骨架逐层添加1.4 方向、曲率与避障1.5 筛选与整理连接1.6 原始文件完整流程1.7 弦图综合展示模块二『共线性图』部分
2.1 复用弦图的数据2.2 只替换坐标系,再逐层添加2.3 跨行连接、避障与比例尺2.4 比较基因邻域2.5 局部、锚定与分段2.6 共线性综合展示模块三『质粒图』部分
3.1 DNA、注释与13个参考序列3.2 从圆圈到多层注释3.3 识别特征、引物与酶切3.4 13个质粒参考案例3.5 质粒综合实战按需查阅:数据与图层
数据与坐标导入和转换数据导入核酸和蛋白比对将蛋白区间转换为基因组坐标绘制注释与处理重叠放置和调整标签添加数据轨道设置配色、图例和主题按序列和链设置参数调整图形预览和保存图形学习地图与函数查阅
使用教程函数文档示例图集常见问题迁移到候选 API术语说明更新日志完整绘图主题。除普通 ggplot2 元素外,控制自动序列轴、弦图标签及各角色图例的外观和位置。配色、刻度、标签和图例顺序仍由标度/图例负责。
用法
代码
theme_ggchord(
axis = NULL,
axis.line = NULL,
axis.ticks = NULL,
axis.minor.ticks = NULL,
axis.text = NULL,
axis.gap = NULL,
axis.ticks.length = NULL,
axis.minor.ticks.length = NULL,
axis.text.offset = NULL,
axis.text.orientation = NULL,
axis.text.check.overlap = NULL,
seq.label = NULL,
gene.label = NULL,
gene.label.segment = NULL,
feature.label = NULL,
feature.label.segment = NULL,
restriction.label = NULL,
restriction.label.segment = NULL,
seq.center.label = NULL,
seq.center.name = NULL,
seq.center.length = NULL,
legend.seq = NULL,
legend.seq.position = NULL,
legend.seq.direction = NULL,
legend.seq.background = NULL,
legend.seq.key = NULL,
legend.seq.key.size = NULL,
legend.seq.key.width = NULL,
legend.seq.key.height = NULL,
legend.seq.text = NULL,
legend.seq.text.position = NULL,
legend.seq.title = NULL,
legend.seq.title.position = NULL,
legend.seq.margin = NULL,
legend.seq.spacing = NULL,
legend.link = NULL,
legend.link.position = NULL,
legend.link.direction = NULL,
legend.link.background = NULL,
legend.link.key = NULL,
legend.link.key.size = NULL,
legend.link.key.width = NULL,
legend.link.key.height = NULL,
legend.link.text = NULL,
legend.link.text.position = NULL,
legend.link.title = NULL,
legend.link.title.position = NULL,
legend.link.margin = NULL,
legend.link.spacing = NULL,
legend.ribbon = NULL,
legend.ribbon.position = NULL,
legend.ribbon.direction = NULL,
legend.ribbon.background = NULL,
legend.ribbon.key = NULL,
legend.ribbon.key.size = NULL,
legend.ribbon.key.width = NULL,
legend.ribbon.key.height = NULL,
legend.ribbon.text = NULL,
legend.ribbon.text.position = NULL,
legend.ribbon.title = NULL,
legend.ribbon.title.position = NULL,
legend.ribbon.margin = NULL,
legend.ribbon.spacing = NULL,
legend.ribbon.ticks = NULL,
legend.ribbon.ticks.length = NULL,
legend.ribbon.axis.line = NULL,
legend.gene = NULL,
legend.gene.position = NULL,
legend.gene.direction = NULL,
legend.gene.background = NULL,
legend.gene.key = NULL,
legend.gene.key.size = NULL,
legend.gene.key.width = NULL,
legend.gene.key.height = NULL,
legend.gene.text = NULL,
legend.gene.text.position = NULL,
legend.gene.title = NULL,
legend.gene.title.position = NULL,
legend.gene.margin = NULL,
legend.gene.spacing = NULL,
legend.feature = NULL,
legend.feature.position = NULL,
legend.feature.direction = NULL,
legend.feature.background = NULL,
legend.feature.key = NULL,
legend.feature.key.size = NULL,
legend.feature.key.width = NULL,
legend.feature.key.height = NULL,
legend.feature.text = NULL,
legend.feature.text.position = NULL,
legend.feature.title = NULL,
legend.feature.title.position = NULL,
legend.feature.margin = NULL,
legend.feature.spacing = NULL,
legend.region = NULL,
legend.region.position = NULL,
legend.region.direction = NULL,
legend.region.background = NULL,
legend.region.key = NULL,
legend.region.key.size = NULL,
legend.region.key.width = NULL,
legend.region.key.height = NULL,
legend.region.text = NULL,
legend.region.text.position = NULL,
legend.region.title = NULL,
legend.region.title.position = NULL,
legend.region.margin = NULL,
legend.region.spacing = NULL,
...
)
theme_ggchord_minimal(
axis = NULL,
axis.line = NULL,
axis.ticks = NULL,
axis.minor.ticks = NULL,
axis.text = NULL,
axis.gap = NULL,
axis.ticks.length = NULL,
axis.minor.ticks.length = NULL,
axis.text.offset = NULL,
axis.text.orientation = NULL,
axis.text.check.overlap = NULL,
seq.label = NULL,
gene.label = NULL,
gene.label.segment = NULL,
feature.label = NULL,
feature.label.segment = NULL,
restriction.label = NULL,
restriction.label.segment = NULL,
seq.center.label = NULL,
seq.center.name = NULL,
seq.center.length = NULL,
legend.seq = NULL,
legend.seq.position = NULL,
legend.seq.direction = NULL,
legend.seq.background = NULL,
legend.seq.key = NULL,
legend.seq.key.size = NULL,
legend.seq.key.width = NULL,
legend.seq.key.height = NULL,
legend.seq.text = NULL,
legend.seq.text.position = NULL,
legend.seq.title = NULL,
legend.seq.title.position = NULL,
legend.seq.margin = NULL,
legend.seq.spacing = NULL,
legend.link = NULL,
legend.link.position = NULL,
legend.link.direction = NULL,
legend.link.background = NULL,
legend.link.key = NULL,
legend.link.key.size = NULL,
legend.link.key.width = NULL,
legend.link.key.height = NULL,
legend.link.text = NULL,
legend.link.text.position = NULL,
legend.link.title = NULL,
legend.link.title.position = NULL,
legend.link.margin = NULL,
legend.link.spacing = NULL,
legend.ribbon = NULL,
legend.ribbon.position = NULL,
legend.ribbon.direction = NULL,
legend.ribbon.background = NULL,
legend.ribbon.key = NULL,
legend.ribbon.key.size = NULL,
legend.ribbon.key.width = NULL,
legend.ribbon.key.height = NULL,
legend.ribbon.text = NULL,
legend.ribbon.text.position = NULL,
legend.ribbon.title = NULL,
legend.ribbon.title.position = NULL,
legend.ribbon.margin = NULL,
legend.ribbon.spacing = NULL,
legend.ribbon.ticks = NULL,
legend.ribbon.ticks.length = NULL,
legend.ribbon.axis.line = NULL,
legend.gene = NULL,
legend.gene.position = NULL,
legend.gene.direction = NULL,
legend.gene.background = NULL,
legend.gene.key = NULL,
legend.gene.key.size = NULL,
legend.gene.key.width = NULL,
legend.gene.key.height = NULL,
legend.gene.text = NULL,
legend.gene.text.position = NULL,
legend.gene.title = NULL,
legend.gene.title.position = NULL,
legend.gene.margin = NULL,
legend.gene.spacing = NULL,
legend.feature = NULL,
legend.feature.position = NULL,
legend.feature.direction = NULL,
legend.feature.background = NULL,
legend.feature.key = NULL,
legend.feature.key.size = NULL,
legend.feature.key.width = NULL,
legend.feature.key.height = NULL,
legend.feature.text = NULL,
legend.feature.text.position = NULL,
legend.feature.title = NULL,
legend.feature.title.position = NULL,
legend.feature.margin = NULL,
legend.feature.spacing = NULL,
legend.region = NULL,
legend.region.position = NULL,
legend.region.direction = NULL,
legend.region.background = NULL,
legend.region.key = NULL,
legend.region.key.size = NULL,
legend.region.key.width = NULL,
legend.region.key.height = NULL,
legend.region.text = NULL,
legend.region.text.position = NULL,
legend.region.title = NULL,
legend.region.title.position = NULL,
legend.region.margin = NULL,
legend.region.spacing = NULL,
...
)
theme_ggchord_dark(
axis = NULL,
axis.line = NULL,
axis.ticks = NULL,
axis.minor.ticks = NULL,
axis.text = NULL,
axis.gap = NULL,
axis.ticks.length = NULL,
axis.minor.ticks.length = NULL,
axis.text.offset = NULL,
axis.text.orientation = NULL,
axis.text.check.overlap = NULL,
seq.label = NULL,
gene.label = NULL,
gene.label.segment = NULL,
feature.label = NULL,
feature.label.segment = NULL,
restriction.label = NULL,
restriction.label.segment = NULL,
seq.center.label = NULL,
seq.center.name = NULL,
seq.center.length = NULL,
legend.seq = NULL,
legend.seq.position = NULL,
legend.seq.direction = NULL,
legend.seq.background = NULL,
legend.seq.key = NULL,
legend.seq.key.size = NULL,
legend.seq.key.width = NULL,
legend.seq.key.height = NULL,
legend.seq.text = NULL,
legend.seq.text.position = NULL,
legend.seq.title = NULL,
legend.seq.title.position = NULL,
legend.seq.margin = NULL,
legend.seq.spacing = NULL,
legend.link = NULL,
legend.link.position = NULL,
legend.link.direction = NULL,
legend.link.background = NULL,
legend.link.key = NULL,
legend.link.key.size = NULL,
legend.link.key.width = NULL,
legend.link.key.height = NULL,
legend.link.text = NULL,
legend.link.text.position = NULL,
legend.link.title = NULL,
legend.link.title.position = NULL,
legend.link.margin = NULL,
legend.link.spacing = NULL,
legend.ribbon = NULL,
legend.ribbon.position = NULL,
legend.ribbon.direction = NULL,
legend.ribbon.background = NULL,
legend.ribbon.key = NULL,
legend.ribbon.key.size = NULL,
legend.ribbon.key.width = NULL,
legend.ribbon.key.height = NULL,
legend.ribbon.text = NULL,
legend.ribbon.text.position = NULL,
legend.ribbon.title = NULL,
legend.ribbon.title.position = NULL,
legend.ribbon.margin = NULL,
legend.ribbon.spacing = NULL,
legend.ribbon.ticks = NULL,
legend.ribbon.ticks.length = NULL,
legend.ribbon.axis.line = NULL,
legend.gene = NULL,
legend.gene.position = NULL,
legend.gene.direction = NULL,
legend.gene.background = NULL,
legend.gene.key = NULL,
legend.gene.key.size = NULL,
legend.gene.key.width = NULL,
legend.gene.key.height = NULL,
legend.gene.text = NULL,
legend.gene.text.position = NULL,
legend.gene.title = NULL,
legend.gene.title.position = NULL,
legend.gene.margin = NULL,
legend.gene.spacing = NULL,
legend.feature = NULL,
legend.feature.position = NULL,
legend.feature.direction = NULL,
legend.feature.background = NULL,
legend.feature.key = NULL,
legend.feature.key.size = NULL,
legend.feature.key.width = NULL,
legend.feature.key.height = NULL,
legend.feature.text = NULL,
legend.feature.text.position = NULL,
legend.feature.title = NULL,
legend.feature.title.position = NULL,
legend.feature.margin = NULL,
legend.feature.spacing = NULL,
legend.region = NULL,
legend.region.position = NULL,
legend.region.direction = NULL,
legend.region.background = NULL,
legend.region.key = NULL,
legend.region.key.size = NULL,
legend.region.key.width = NULL,
legend.region.key.height = NULL,
legend.region.text = NULL,
legend.region.text.position = NULL,
legend.region.title = NULL,
legend.region.title.position = NULL,
legend.region.margin = NULL,
legend.region.spacing = NULL,
...
)
theme_ggchord_publication(
axis = NULL,
axis.line = NULL,
axis.ticks = NULL,
axis.minor.ticks = NULL,
axis.text = NULL,
axis.gap = NULL,
axis.ticks.length = NULL,
axis.minor.ticks.length = NULL,
axis.text.offset = NULL,
axis.text.orientation = NULL,
axis.text.check.overlap = NULL,
seq.label = NULL,
gene.label = NULL,
gene.label.segment = NULL,
feature.label = NULL,
feature.label.segment = NULL,
restriction.label = NULL,
restriction.label.segment = NULL,
seq.center.label = NULL,
seq.center.name = NULL,
seq.center.length = NULL,
legend.seq = NULL,
legend.seq.position = NULL,
legend.seq.direction = NULL,
legend.seq.background = NULL,
legend.seq.key = NULL,
legend.seq.key.size = NULL,
legend.seq.key.width = NULL,
legend.seq.key.height = NULL,
legend.seq.text = NULL,
legend.seq.text.position = NULL,
legend.seq.title = NULL,
legend.seq.title.position = NULL,
legend.seq.margin = NULL,
legend.seq.spacing = NULL,
legend.link = NULL,
legend.link.position = NULL,
legend.link.direction = NULL,
legend.link.background = NULL,
legend.link.key = NULL,
legend.link.key.size = NULL,
legend.link.key.width = NULL,
legend.link.key.height = NULL,
legend.link.text = NULL,
legend.link.text.position = NULL,
legend.link.title = NULL,
legend.link.title.position = NULL,
legend.link.margin = NULL,
legend.link.spacing = NULL,
legend.ribbon = NULL,
legend.ribbon.position = NULL,
legend.ribbon.direction = NULL,
legend.ribbon.background = NULL,
legend.ribbon.key = NULL,
legend.ribbon.key.size = NULL,
legend.ribbon.key.width = NULL,
legend.ribbon.key.height = NULL,
legend.ribbon.text = NULL,
legend.ribbon.text.position = NULL,
legend.ribbon.title = NULL,
legend.ribbon.title.position = NULL,
legend.ribbon.margin = NULL,
legend.ribbon.spacing = NULL,
legend.ribbon.ticks = NULL,
legend.ribbon.ticks.length = NULL,
legend.ribbon.axis.line = NULL,
legend.gene = NULL,
legend.gene.position = NULL,
legend.gene.direction = NULL,
legend.gene.background = NULL,
legend.gene.key = NULL,
legend.gene.key.size = NULL,
legend.gene.key.width = NULL,
legend.gene.key.height = NULL,
legend.gene.text = NULL,
legend.gene.text.position = NULL,
legend.gene.title = NULL,
legend.gene.title.position = NULL,
legend.gene.margin = NULL,
legend.gene.spacing = NULL,
legend.feature = NULL,
legend.feature.position = NULL,
legend.feature.direction = NULL,
legend.feature.background = NULL,
legend.feature.key = NULL,
legend.feature.key.size = NULL,
legend.feature.key.width = NULL,
legend.feature.key.height = NULL,
legend.feature.text = NULL,
legend.feature.text.position = NULL,
legend.feature.title = NULL,
legend.feature.title.position = NULL,
legend.feature.margin = NULL,
legend.feature.spacing = NULL,
legend.region = NULL,
legend.region.position = NULL,
legend.region.direction = NULL,
legend.region.background = NULL,
legend.region.key = NULL,
legend.region.key.size = NULL,
legend.region.key.width = NULL,
legend.region.key.height = NULL,
legend.region.text = NULL,
legend.region.text.position = NULL,
legend.region.title = NULL,
legend.region.title.position = NULL,
legend.region.margin = NULL,
legend.region.spacing = NULL,
...
)
theme_ggchord_plasmid(
axis = NULL,
axis.line = NULL,
axis.ticks = NULL,
axis.minor.ticks = NULL,
axis.text = NULL,
axis.gap = NULL,
axis.ticks.length = NULL,
axis.minor.ticks.length = NULL,
axis.text.offset = NULL,
axis.text.orientation = NULL,
axis.text.check.overlap = NULL,
seq.label = NULL,
gene.label = NULL,
gene.label.segment = NULL,
feature.label = NULL,
feature.label.segment = NULL,
restriction.label = NULL,
restriction.label.segment = NULL,
seq.center.label = NULL,
seq.center.name = NULL,
seq.center.length = NULL,
legend.seq = NULL,
legend.seq.position = NULL,
legend.seq.direction = NULL,
legend.seq.background = NULL,
legend.seq.key = NULL,
legend.seq.key.size = NULL,
legend.seq.key.width = NULL,
legend.seq.key.height = NULL,
legend.seq.text = NULL,
legend.seq.text.position = NULL,
legend.seq.title = NULL,
legend.seq.title.position = NULL,
legend.seq.margin = NULL,
legend.seq.spacing = NULL,
legend.link = NULL,
legend.link.position = NULL,
legend.link.direction = NULL,
legend.link.background = NULL,
legend.link.key = NULL,
legend.link.key.size = NULL,
legend.link.key.width = NULL,
legend.link.key.height = NULL,
legend.link.text = NULL,
legend.link.text.position = NULL,
legend.link.title = NULL,
legend.link.title.position = NULL,
legend.link.margin = NULL,
legend.link.spacing = NULL,
legend.ribbon = NULL,
legend.ribbon.position = NULL,
legend.ribbon.direction = NULL,
legend.ribbon.background = NULL,
legend.ribbon.key = NULL,
legend.ribbon.key.size = NULL,
legend.ribbon.key.width = NULL,
legend.ribbon.key.height = NULL,
legend.ribbon.text = NULL,
legend.ribbon.text.position = NULL,
legend.ribbon.title = NULL,
legend.ribbon.title.position = NULL,
legend.ribbon.margin = NULL,
legend.ribbon.spacing = NULL,
legend.ribbon.ticks = NULL,
legend.ribbon.ticks.length = NULL,
legend.ribbon.axis.line = NULL,
legend.gene = NULL,
legend.gene.position = NULL,
legend.gene.direction = NULL,
legend.gene.background = NULL,
legend.gene.key = NULL,
legend.gene.key.size = NULL,
legend.gene.key.width = NULL,
legend.gene.key.height = NULL,
legend.gene.text = NULL,
legend.gene.text.position = NULL,
legend.gene.title = NULL,
legend.gene.title.position = NULL,
legend.gene.margin = NULL,
legend.gene.spacing = NULL,
legend.feature = NULL,
legend.feature.position = NULL,
legend.feature.direction = NULL,
legend.feature.background = NULL,
legend.feature.key = NULL,
legend.feature.key.size = NULL,
legend.feature.key.width = NULL,
legend.feature.key.height = NULL,
legend.feature.text = NULL,
legend.feature.text.position = NULL,
legend.feature.title = NULL,
legend.feature.title.position = NULL,
legend.feature.margin = NULL,
legend.feature.spacing = NULL,
legend.region = NULL,
legend.region.position = NULL,
legend.region.direction = NULL,
legend.region.background = NULL,
legend.region.key = NULL,
legend.region.key.size = NULL,
legend.region.key.width = NULL,
legend.region.key.height = NULL,
legend.region.text = NULL,
legend.region.text.position = NULL,
legend.region.title = NULL,
legend.region.title.position = NULL,
legend.region.margin = NULL,
legend.region.spacing = NULL,
...
)参数
- axis
NULL显示自动序列轴,ggplot2::element_blank()隐藏整组轴装饰。- axis.line, axis.ticks, axis.minor.ticks
坐标轴线元素。
- axis.text
坐标轴文字元素。
- axis.gap, axis.ticks.length, axis.minor.ticks.length, axis.text.offset
控制物理轴间距的单值
grid::unit()对象。负axis.gap将圆图刻度及标签移到序列环内侧,质粒预设采用此约定。- axis.text.orientation
支持
"horizontal"、"parallel"、"perpendicular"或有限数值角度。- axis.text.check.overlap
是否隐藏重叠坐标轴标签。
- seq.label, gene.label, feature.label, restriction.label, seq.center.label, seq.center.name, seq.center.length
序列、基因、通用注释、酶切及圆图中心标签的文字元素。
- gene.label.segment, feature.label.segment, restriction.label.segment
基因、注释及酶切引导线的线元素。
- legend.seq, legend.ribbon, legend.gene, legend.feature, legend.region
NULL显示并继承公共设置,ggplot2::element_blank()隐藏该角色的全部图例。- legend.seq.position, legend.ribbon.position, legend.gene.position, legend.feature.position, legend.region.position
各角色图例位置。
- legend.seq.direction, legend.ribbon.direction, legend.gene.direction, legend.feature.direction, legend.region.direction
各角色图例方向。
- legend.seq.background, legend.ribbon.background, legend.gene.background, legend.feature.background, legend.region.background
各角色图例背景。
- legend.seq.key, legend.ribbon.key, legend.gene.key, legend.feature.key, legend.region.key
各角色图例键元素。
- legend.seq.key.size, legend.seq.key.width, legend.seq.key.height, legend.ribbon.key.size, legend.ribbon.key.width, legend.ribbon.key.height, legend.gene.key.size, legend.gene.key.width, legend.gene.key.height, legend.feature.key.size, legend.feature.key.width, legend.feature.key.height, legend.region.key.size, legend.region.key.width, legend.region.key.height
各角色图例键尺寸。
- legend.seq.text, legend.ribbon.text, legend.gene.text, legend.feature.text, legend.region.text
各角色图例文字元素。
- legend.seq.text.position, legend.ribbon.text.position, legend.gene.text.position, legend.feature.text.position, legend.region.text.position
各角色图例文字位置。
- legend.seq.title, legend.ribbon.title, legend.gene.title, legend.feature.title, legend.region.title
各角色图例标题元素。
- legend.seq.title.position, legend.ribbon.title.position, legend.gene.title.position, legend.feature.title.position, legend.region.title.position
各角色图例标题位置。
- legend.seq.margin, legend.ribbon.margin, legend.gene.margin, legend.feature.margin, legend.region.margin
各角色图例边距。
- legend.seq.spacing, legend.ribbon.spacing, legend.gene.spacing, legend.feature.spacing, legend.region.spacing
各角色图例间距。
- legend.link, legend.link.position, legend.link.direction, legend.link.background, legend.link.key, legend.link.key.size, legend.link.key.width, legend.link.key.height, legend.link.text, legend.link.text.position, legend.link.title, legend.link.title.position, legend.link.margin, legend.link.spacing
点连接图例外观,遵循相同角色专属规则。
- legend.ribbon.ticks, legend.ribbon.axis.line
区间连接颜色条线元素。
- legend.ribbon.ticks.length
区间连接颜色条刻度长度。
- ...
标准 ggplot2 主题参数,包括公共文字、图及图例设置;公共图例设置也提供角色继承。已删除的下划线风格参数会给出迁移错误。
外观设置
普通文字、面板、标题及共享图例遵循 ggplot2。序列轴设置控制自动装饰,不选择基因组刻度;刻度和标签使用 scale_seq_position_continuous()。角色文字及引导线元素设置非数据注释样式,角色图例继承公共外观;标度/图例对象仍负责配色、刻度及顺序。物理间距要求单值绝对 grid::unit(),axis.text.orientation 也是单值。预设主题共享该签名并提供外观默认值。
