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Create a Circular Layout for Genomic Data

Source: R/layout-chain-circle-genomic.R
circle_genomic.Rd

circle_genomic() constructs a circular layout specifically for genomic data. It is a specialized variant of circle_continuous() that applies default axis limits and coerces the first column of each plot's data to use chromosome (seqname) identifiers-matching those in the layout data-as factor levels.

Usage

circle_genomic(
  data,
  ...,
  radial = NULL,
  direction = "outward",
  sector_spacing = NULL,
  theme = NULL
)

Arguments

data

The input data, which can be:

  • A character string ("hg19" or "hg38") to load a predefined cytoband reference.

  • A data.frame with at least three columns: chromosome, start, and end positions.

  • A genomic object convertible via fortify_data_frame().

...

Additional arguments passed to specific methods or fortify_data_frame().

radial

A coord_circle()/coord_radial() object that defines the global parameters for coordinate across all plots in the layout. The parameters start, end, direction, and expand will be inherited and applied uniformly to all plots within the layout. The parameters theta and r.axis.inside will always be ignored and will be set to "x" and TRUE, respectively, for all plots.

direction

A single string of "inward" or "outward", indicating the direction in which the plot is added.

  • outward: The plot is added from the inner to the outer.

  • inward: The plot is added from the outer to the inner.

sector_spacing

The size of spacing between different panel. A numeric of the radians or a rel() object.

theme

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

Value

A circle_layout object representing the genomic layout.