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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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

适用于 ggchord 的部分 ggplot2 辅助函数

本页目录

• 用法
• 参数
• 详细说明

映射中的美学表达式；x 在阶段映射或相对大小函数中分别表示表达式或相对倍数。

用法

代码

aes(x, y, ...)

after_stat(x)

after_scale(x)

annotate(
  geom,
  x = NULL,
  y = NULL,
  xmin = NULL,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  xend = NULL,
  yend = NULL,
  ...,
  na.rm = FALSE
)

labs(
  ...,
  title = waiver(),
  subtitle = waiver(),
  caption = waiver(),
  tag = waiver(),
  dictionary = waiver(),
  alt = waiver(),
  alt_insight = waiver()
)

ggtitle(label, subtitle = waiver())

guides(...)

theme(
  ...,
  line,
  rect,
  text,
  title,
  point,
  polygon,
  geom,
  spacing,
  margins,
  aspect.ratio,
  axis.title,
  axis.title.x,
  axis.title.x.top,
  axis.title.x.bottom,
  axis.title.y,
  axis.title.y.left,
  axis.title.y.right,
  axis.text,
  axis.text.x,
  axis.text.x.top,
  axis.text.x.bottom,
  axis.text.y,
  axis.text.y.left,
  axis.text.y.right,
  axis.text.theta,
  axis.text.r,
  axis.ticks,
  axis.ticks.x,
  axis.ticks.x.top,
  axis.ticks.x.bottom,
  axis.ticks.y,
  axis.ticks.y.left,
  axis.ticks.y.right,
  axis.ticks.theta,
  axis.ticks.r,
  axis.minor.ticks.x.top,
  axis.minor.ticks.x.bottom,
  axis.minor.ticks.y.left,
  axis.minor.ticks.y.right,
  axis.minor.ticks.theta,
  axis.minor.ticks.r,
  axis.ticks.length,
  axis.ticks.length.x,
  axis.ticks.length.x.top,
  axis.ticks.length.x.bottom,
  axis.ticks.length.y,
  axis.ticks.length.y.left,
  axis.ticks.length.y.right,
  axis.ticks.length.theta,
  axis.ticks.length.r,
  axis.minor.ticks.length,
  axis.minor.ticks.length.x,
  axis.minor.ticks.length.x.top,
  axis.minor.ticks.length.x.bottom,
  axis.minor.ticks.length.y,
  axis.minor.ticks.length.y.left,
  axis.minor.ticks.length.y.right,
  axis.minor.ticks.length.theta,
  axis.minor.ticks.length.r,
  axis.line,
  axis.line.x,
  axis.line.x.top,
  axis.line.x.bottom,
  axis.line.y,
  axis.line.y.left,
  axis.line.y.right,
  axis.line.theta,
  axis.line.r,
  legend.background,
  legend.margin,
  legend.spacing,
  legend.spacing.x,
  legend.spacing.y,
  legend.key,
  legend.key.size,
  legend.key.height,
  legend.key.width,
  legend.key.spacing,
  legend.key.spacing.x,
  legend.key.spacing.y,
  legend.key.justification,
  legend.frame,
  legend.ticks,
  legend.ticks.length,
  legend.axis.line,
  legend.text,
  legend.text.position,
  legend.title,
  legend.title.position,
  legend.position,
  legend.position.inside,
  legend.direction,
  legend.byrow,
  legend.justification,
  legend.justification.top,
  legend.justification.bottom,
  legend.justification.left,
  legend.justification.right,
  legend.justification.inside,
  legend.location,
  legend.box,
  legend.box.just,
  legend.box.margin,
  legend.box.background,
  legend.box.spacing,
  panel.background,
  panel.border,
  panel.spacing,
  panel.spacing.x,
  panel.spacing.y,
  panel.grid,
  panel.grid.major,
  panel.grid.minor,
  panel.grid.major.x,
  panel.grid.major.y,
  panel.grid.minor.x,
  panel.grid.minor.y,
  panel.ontop,
  panel.widths,
  panel.heights,
  plot.background,
  plot.title,
  plot.title.position,
  plot.subtitle,
  plot.caption,
  plot.caption.position,
  plot.tag,
  plot.tag.position,
  plot.tag.location,
  plot.margin,
  strip.background,
  strip.background.x,
  strip.background.y,
  strip.clip,
  strip.placement,
  strip.text,
  strip.text.x,
  strip.text.x.bottom,
  strip.text.x.top,
  strip.text.y,
  strip.text.y.left,
  strip.text.y.right,
  strip.switch.pad.grid,
  strip.switch.pad.wrap,
  complete = FALSE,
  validate = TRUE
)

element_blank()

element_line(
  colour = NULL,
  linewidth = NULL,
  linetype = NULL,
  lineend = NULL,
  color = NULL,
  linejoin = NULL,
  arrow = NULL,
  arrow.fill = NULL,
  inherit.blank = FALSE,
  size = deprecated(),
  ...
)

element_rect(
  fill = NULL,
  colour = NULL,
  linewidth = NULL,
  linetype = NULL,
  color = NULL,
  linejoin = NULL,
  inherit.blank = FALSE,
  size = deprecated(),
  ...
)

element_text(
  family = NULL,
  face = NULL,
  colour = NULL,
  size = NULL,
  hjust = NULL,
  vjust = NULL,
  angle = NULL,
  lineheight = NULL,
  color = NULL,
  margin = NULL,
  debug = NULL,
  inherit.blank = FALSE,
  ...
)

margin(t = 0, r = 0, b = 0, l = 0, unit = "pt", ...)

rel(x)

ggsave(
  filename,
  plot = get_last_plot(),
  device = NULL,
  path = NULL,
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
  ...
)

last_plot()

waiver()

expansion(mult = 0, add = 0)

position_identity()

PositionIdentity

参数

x, y

映射中的美学表达式；x 在阶段映射或相对大小函数中分别表示表达式或相对倍数。

...

根据所调用的函数，传入其他命名映射、图例设置、主题元素、固定注释样式或设备参数。

geom, xmin, xmax, ymin, ymax, xend, yend, na.rm

在 annotate() 中指定几何名称、位置边界和端点，以及是否静默移除缺失值；在 theme() 中，geom 用于设置几何默认样式。

title, subtitle, caption, tag, dictionary, alt, alt_insight, label

图形的标题、副标题、图注和标记；dictionary 替换变量标签，alt/alt_insight 提供无障碍描述。在 theme() 中，title 指定可继承的标题样式。

line, rect, text, point, polygon, spacing, margins, aspect.ratio, axis.title, axis.title.x, axis.title.x.top, axis.title.x.bottom, axis.title.y, axis.title.y.left, axis.title.y.right, axis.text, axis.text.x, axis.text.x.top, axis.text.x.bottom, axis.text.y, axis.text.y.left, axis.text.y.right, axis.text.theta, axis.text.r, axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right, axis.ticks.theta, axis.ticks.r, axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r, axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r, axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r, axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right, axis.line.theta, axis.line.r, legend.background, legend.margin, legend.spacing, legend.spacing.x, legend.spacing.y, legend.key, legend.key.size, legend.key.height, legend.key.width, legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y, legend.key.justification, legend.frame, legend.ticks, legend.ticks.length, legend.axis.line, legend.text, legend.text.position, legend.title, legend.title.position, legend.position, legend.position.inside, legend.direction, legend.byrow, legend.justification, legend.justification.top, legend.justification.bottom, legend.justification.left, legend.justification.right, legend.justification.inside, legend.location, legend.box, legend.box.just, legend.box.margin, legend.box.background, legend.box.spacing, panel.background, panel.border, panel.spacing, panel.spacing.x, panel.spacing.y, panel.grid, panel.grid.major, panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y, panel.ontop, panel.widths, panel.heights, plot.background, plot.title, plot.title.position, plot.subtitle, plot.caption, plot.caption.position, plot.tag, plot.tag.position, plot.tag.location, plot.margin, strip.background, strip.background.x, strip.background.y, strip.clip, strip.placement, strip.text, strip.text.x, strip.text.x.bottom, strip.text.x.top, strip.text.y, strip.text.y.left, strip.text.y.right, strip.switch.pad.grid, strip.switch.pad.wrap, complete, validate

主题元素和布局设置。线、矩形和文字元素控制外观；间距与边距使用物理单位，位置及对齐设置控制摆放。坐标轴、图例、面板、整图和分面条的具体元素继承上级设置。complete 表示完整主题，validate 检查元素类型。各元素的可接受值详见 ggplot2::theme。

colour, linewidth, linetype, lineend, color, linejoin, arrow, arrow.fill, inherit.blank, size, fill, family, face, hjust, vjust, angle, lineheight, margin, debug

元素样式：颜色、填充、线宽和线型、线端及连接、箭头、字体族/字形/字号、对齐、角度、行距和文字边距。inherit.blank 继承上级空白元素；debug 显示文字边界。线和矩形元素的 size 已被上游弃用，请使用 linewidth。

t, r, b, l, unit

上、右、下、左边距及其物理单位。

filename, plot, device, path, scale, width, height, units, dpi, limitsize, bg, create.dir

保存设置：目标文件名与路径、图形、设备、缩放倍数、宽高及单位、栅格分辨率、尺寸限制、背景和是否允许创建目录。

mult, add

标度范围的比例扩展和数值扩展；各接受单值或下界/上界两个值。

详细说明

映射辅助函数为 aes()、after_stat() 和 after_scale()；ggplot2::stage() 组合一个美学属性的多个阶段。使用 labs() 和 ggtitle() 设置标题，guides() 选择图例，theme() 配合 element_*() 设置外观。annotate() 添加固定注释。margin() 和 rel() 指定主题尺寸；waiver() 和 expansion() 指定自动或扩展的标度设置。position_identity() 和 PositionIdentity 为上游原位放置辅助对象。ggsave() 保存指定图形；last_plot() 获取 ggplot2 的上一张图。每个符号均为 ggplot2 原函数或对象，也可用 ggplot2:: 命名空间调用。unit() 和 arrow() 来自 grid。