guide_ideogram_axis: Ideogram axis guide
In teunbrand/ggnomics: ggnomics

Description Usage Arguments Details Value Methods (by generic) See Also Examples

Places an ideogram next to the axis and indicates the data range interpreted as genomic positions on the ideogram. The ideograms need to be setup first with the setup_ideogram() function.

guide_ideogram_axis(
  title = waiver(),
  check.overlap = FALSE,
  angle = NULL,
  n.dodge = 1,
  order = 0,
  position = waiver(),
  chromosome = NULL,
  genome = NULL,
  ideo_size = unit(0.5, "cm"),
  funnel_size = unit(0.5, "cm"),
  funnel_col = "dodgerblue",
  regular_axis = TRUE
)

`title`	A character string or expression indicating a title of guide. If `NULL`, the title is not shown. By default (`waiver()`), the name of the scale object or the name specified in `labs()` is used for the title.
`check.overlap`	silently remove overlapping labels, (recursively) prioritizing the first, last, and middle labels.
`angle`	Compared to setting the angle in `theme()` / `element_text()`, this also uses some heuristics to automatically pick the `hjust` and `vjust` that you probably want.
`n.dodge`	The number of rows (for vertical axes) or columns (for horizontal axes) that should be used to render the labels. This is useful for displaying labels that would otherwise overlap.
`order`	Used to determine the order of the guides (left-to-right, top-to-bottom), if more than one guide must be drawn at the same location.
`position`	Where this guide should be drawn: one of top, bottom, left, or right.
`chromosome`	A `character` with chromosome name of length one, for example `"chr12"`.
`genome`	A `character` with a genome name of length one, for example `"hg38"`.
`ideo_size`	A `unit` of length one indicating the size of the ideogram. If a `numeric` is provided, this is interpreted as millimetre units. A small proportional margin will be added for an indicator.
`funnel_size`	A `unit` of length one indicating the size of the funnel space. If a `numeric` is provided, this is interpreted as millimetre units. If this can be interpreted as zero, no funnel will be drawn.
`funnel_col`	A `character` of length one setting the colour for the funnel and indicator. Set to `NA` to make the funnel and indicator transparent.
`regular_axis`	A `logical` of length one: should the ticks and labels of the usual position axis be drawn? (default: `TRUE`).

Currently does not support S4Vector or genomic scales (yet).

A list with the S3 class guide.

guide_train: Trainer for ideogram axis. See guide-exts.
guide_transform: Transformer for ideogram axis. See guide-exts.
guide_gengrob: Graphic object generator for ideogram axis. See guide-exts.

The setup_ideograms() function for importing and caching ideogram data.

Other position guides: guide_genomic_axis()

# Setup ideograms and make a basic plot
setup_ideograms(genome = "hg38")
p <- ggplot(iris, aes(Sepal.Width * 1e7, Sepal.Length * 1e7)) +
    geom_point()

# As main axis
p + guides(x = guide_ideogram_axis("hg38", chromosome = "chr2"))

# As secundary axis
p + guides(x.sec = guide_ideogram_axis("hg38", chromosome = "chr2",
                                       regular_axis = FALSE))

# Without funnel
p + guides(x = guide_ideogram_axis("hg38", chromosome = "chr2",
                                   funnel_size = 0))

# Without funnel or indicator
p + guides(x = guide_ideogram_axis("hg38", chromosome = "chr2",
                                   funnel_size = 0, funnel_col = NA))