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Add an aligned cytoband ideogram plot

Source: R/plot-ideogram.R
plot_ideogram.Rd

Creates a cytoband ideogram-typically representing chromosome banding patterns-and aligns it within a genomic layout.

Cytoband features (gieStain) are mapped to fill colors following standard cytogenetic conventions (e.g., gpos, gneg, acen, stalk). Optionally, chromosome names can be displayed as labels.

Usage

plot_ideogram(
  mapping = aes(),
  ...,
  seqnames = NULL,
  size = NULL,
  active = NULL
)

Arguments

mapping

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

...

Arguments passed on to ggplot2::geom_text

stat

The statistical transformation to use on the data for this layer. When using a geom_*() function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

  • For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

  • For more information and other ways to specify the position, see the layer position documentation.

parse

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

size.unit

How the size aesthetic is interpreted: as millimetres ("mm", default), points ("pt"), centimetres ("cm"), inches ("in"), or picas ("pc").

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. annotation_borders().

check_overlap

If TRUE, text that overlaps previous text in the same layer will not be plotted. check_overlap happens at draw time and in the order of the data. Therefore data should be arranged by the label column before calling geom_text(). Note that this argument is not supported by geom_label().

seqnames

A single logical or numeric value controlling chromosome label display. Defaults to TRUE.

  • Logical (TRUE/FALSE):

    • TRUE: display labels at the default offset:

      • 1 above the ideogram (vertical layout)

      • -1 below the ideogram (horizontal layout)

    • FALSE: do not display labels.

  • Numeric: Specifies the vertical position of labels relative to the ideogram’s y-axis:

    • Positive: above the ideogram (offset from the upper border)

    • Negative: below the ideogram (offset from the lower border)

    • 0: centered.

Note: The cytoband vertical range spans from 0 to 1.

size

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

active

A active() object that defines the context settings when added to a layout.