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.
plot_ideogram(
mapping = aes(),
...,
seqnames = NULL,
size = NULL,
active = NULL
)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
statThe 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.
positionA 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.
parseIf TRUE, the labels will be parsed into expressions and
displayed as described in ?plotmath.
size.unitHow the size aesthetic is interpreted: as millimetres
("mm", default), points ("pt"), centimetres ("cm"), inches ("in"),
or picas ("pc").
na.rmIf FALSE, the default, missing values are removed with
a warning. If TRUE, missing values are silently removed.
show.legendlogical. 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.aesIf 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_overlapIf 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().
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.
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.
A active() object that defines the context settings when
added to a layout.