Draw a map which represents positions of different chromosomes on the curve

# S4 method for GenomicHilbertCurve
hc_map(object, level = 7,
    fill = rand_color(length(background), transparency = 0.5), border = NA,
    labels = names(object@background), show_labels = TRUE, labels_gp = gpar(),
    add = FALSE, ...)

Arguments

object: a GenomicHilbertCurve-class object
level: Since a map does not need to have high resolution, a value of around 7 would be enough. If add is set to TRUE, level will be enforced to have the same level in the current Hilbert curve.
fill: colors for different chromosomes, or more generally, for different 'seqnames'.
border: colors for the borders of chromosomes. Set it to NA if borders are suppressed.
labels: label for each chromosome, or more generally, for different 'sequences'
show_labels: whether show text labels
labels_gp: graphic settings for labels
add: whether add the map to the current curve or draw it in a new graphic device. Notice if add is set to TRUE, you should set fill with transparency so that it will not hide your original plot.
...: pass to GenomicHilbertCurve. It is only used if you want the map to be plotted in a new graphic device.

Details

When multiple genomic categories (e.g. chromosomes) are drawn into one single Hilbert curve, a map which shows the positions of categories on the curve is necessary to distinguish different genomic categories.

Under "pixel" mode, if the map is directly added to the Hilbert curve, no chromosome name is drawn. The chromosome names are only drawn if the map is plotted in a new graphic device or added to the Hilbert curve under "normal" mode.

Just be careful if you directly overlay the map to the curve that the color of the map does not affect the original plot too much.

Value

A GenomicHilbertCurve-class object

Author

Zuguang Gu <z.gu@dkfz.de>

Examples

require(circlize)
require(GenomicRanges)
bed = generateRandomBed(nr = 100)
gr = GRanges(seqnames = bed[[1]], ranges = IRanges(bed[[2]], bed[[3]]))
hc = GenomicHilbertCurve()
hc_points(hc, gr, gp = gpar(fill = rand_color(length(gr))))
# add it in the same graphic device
hc_map(hc, fill = rand_color(24, transparency = 0.5), add = TRUE)


# add the map only with borders
hc = GenomicHilbertCurve()
hc_points(hc, gr, gp = gpar(fill = rand_color(length(gr))))
hc_map(hc, fill = NA, border = "grey", add = TRUE)


# or open a new graphic device
hc_map(hc, fill = rand_color(24))