circos.genomicAxis {circlize}

Add genomic axes

Description

Add genomic axes

Usage

circos.genomicAxis(
    h = "top",
    major.at = NULL,
    labels = NULL,
    major.by = NULL,
    tickLabelsStartFromZero = TRUE,
    labels.cex = 0.4*par("cex"),
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    ...)

Arguments

h

Position of the axes. "top" or "bottom".

major.at

Major breaks. If major.at is set, major.by is ignored.

labels

labels corresponding to major.at. If labels is set, major.at must be set.

major.by

Increment of major ticks. It is calculated automatically if the value is not set (about every 10 degrees there is a major tick).

tickLabelsStartFromZero

Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.

labels.cex

The font size for the axis tick labels.

sector.index

Index for the sector

track.index

Index for the track

...

Other arguments pass to circos.axis.

Details

It assigns proper tick labels under genomic coordinate.

See Also

https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#genomic-axes

Examples

circos.initializeWithIdeogram(chromosome.index = paste0("chr", 1:4), plotType = NULL)
circos.track(ylim = c(0, 1), panel.fun = function(x, y) circos.genomicAxis())
circos.track(ylim = c(0, 1), track.height = 0.1)
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
    circos.genomicAxis(h = "bottom", direction = "inside")
})
circos.clear()