Add a new layer to the Hilbert curve

# S4 method for GenomicHilbertCurve
hc_layer(object, gr, col = "red", border = NA,
    mean_mode = c("w0", "absolute", "weighted", "max_freq"), grid_line = 0,
    grid_line_col = "black", overlay = default_overlay)

Arguments

object: a GenomicHilbertCurve-class object
gr: a GRanges object which contains the genomic regions to be mapped to the curve
col: a scalar or a vector of colors which correspond to regions in gr, pass to hc_layer,HilbertCurve-method
border: a scalar or a vector of colors which correspond to the borders of regions. Set it to NA if borders are suppressed.
mean_mode: Under 'pixel' mode, each pixel represents a small window. This argument provides methods to summarize value for the small window if the input genomic regions can not completely overlap with the window, pass to hc_layer,HilbertCurve-method
grid_line: whether add grid lines to show blocks of the Hilber curve, pass to hc_layer,HilbertCurve-method
grid_line_col: color for the grid lines, pass to hc_layer,HilbertCurve-method
overlay: a self-defined function which defines how to overlay new layer to the plot, pass to hc_layer,HilbertCurve-method

Details

It is basically a wrapper of hc_layer,HilbertCurve-method.

Value

Refer to hc_layer,HilbertCurve-method

Author

Zuguang Gu <z.gu@dkfz.de>

Examples

require(circlize)
require(GenomicRanges)
bed = generateRandomBed()
gr = GRanges(seqnames = bed[[1]], ranges = IRanges(bed[[2]], bed[[3]]))
hc = GenomicHilbertCurve(mode = "pixel", level = 9)
hc_layer(hc, gr, col = rand_color(length(gr)))