plot_ideogram: Add an aligned cytoband ideogram plot
In ggalign: A 'ggplot2' Extension for Composable Visualization

plot_ideogram

R Documentation

Add an aligned cytoband ideogram plot

Description

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.