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0.16.6 文档

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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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。

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。

返回值

携带 ggchord 外观设置的完整 ggplot2 主题。

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。

标准 ggplot2 设置

通过 ... 仍可设置标准文字、图标题/说明/标签、背景、图边距及公共图例,例如 theme_ggchord(text = element_text(size = 12))。仅 ggchord 专属设置列为显式形参供 IDE 补全;若 IDE 额外展开上游 dots,可能仍显示上游建议,本包只控制自己的函数签名。