HilbertCurve (version 1.2.2)

hc_map-GenomicHilbertCurve-method: Draw a map which represents positions of different chromosomes on the curve

Description

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

Usage

## S3 method for class 'GenomicHilbertCurve':
hc_map(object, level = 7,
    fill = rand_color(length(background), transparency = 0.5), border = NA,
    labels = names(object@background), 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'

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.

Value

• A GenomicHilbertCurve-class object

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.

Examples

require(circlize)
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))