0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Selected ggplot2 helpers for ggchord plots

On this page

• Usage
• Arguments
• Details

ggchord re-exports a deliberately small set of ggplot2 helpers that are directly useful when constructing, annotating, styling, or saving a chord plot. Cartesian geoms, coordinates, facets, generic scales, and complete theme presets remain in ggplot2 so IDE completion stays focused.

Usage

Code

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

Arguments

x, y

Aesthetic expressions for mappings; x is also the staged expression or relative size, depending on the helper.

...

Additional named mappings, guide specifications, theme elements, fixed annotation aesthetics or device arguments, as appropriate for the called helper.

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

For annotate(), the geometry name, positional bounds and endpoints, and whether missing values are removed silently. In theme(), geom instead sets geometry defaults.

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

Plot labels, title, subtitle, caption and tag; dictionary replaces variable labels and alt/alt_insight provide accessible descriptions. In theme(), title supplies inherited title styling.

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

Theme elements and layout settings. Line, rectangle and text elements control appearance; spacing and margins use physical units, positions and justifications control placement. More specific axis, legend, panel, plot and strip elements inherit from their parents. complete marks a complete theme; validate checks element types. Consult ggplot2::theme for each element and its accepted values.

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

Element styling: colours, fill, line width and type, line ends and joins, arrows, font family/face/size, alignment, angle, line spacing and text margins. inherit.blank follows blank parent elements; debug shows text bounds. size for line/rectangle elements is deprecated upstream; use linewidth.

t, r, b, l, unit

Top, right, bottom and left margins and their physical unit.

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

Save settings: destination filename/path, plot, device, scale multiplier, width/height and units, raster resolution, size limit, background and permission to create the directory.

mult, add

Multiplicative and additive scale expansion, each a single value or lower/upper pair.

Details

Mapping helpers are aes(), after_stat() and after_scale(); ggplot2::stage() combines stages of one aesthetic. Use labs() and ggtitle() for titles, guides() for guide selection, and theme() with the element_*() helpers for appearance. annotate() adds fixed annotations. margin() and rel() specify theme sizes; waiver() and expansion() specify automatic or expanded scale settings. position_identity() and PositionIdentity are the upstream identity placement helpers. ggsave() saves a supplied plot; last_plot() retrieves ggplot2's last plot. Each symbol is the original ggplot2 function or object, and can also be called with its ggplot2:: namespace. unit() and arrow() come from grid.