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Create a stack Layout for Genomic Data

Source: R/layout-chain-stack-genomic.R
stack_genomic.Rd

stack_genomic() constructs a stack layout specifically for genomic data. It is a specialized variant of stack_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

stack_genomic(direction, data = NULL, ..., theme = NULL, sizes = NA)

stack_genomicv(data = NULL, ...)

stack_genomich(data = NULL, ...)

Arguments

direction

A string indicating the direction of the stack layout, either "h"(horizontal) or "v"(vertical).

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().

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.

sizes

A numeric value or a unit object. When used for the quad_layout() annotation, it must be of length 1. When used in the stack_layout() with a nested quad_layout(), it should be of length 3, specifying the relative heights (for direction = "h") or widths (for direction = "v") to be applied to the layout.

Value

A stack_layout object representing the genomic layout.