Add points to a plotting region, specifically for genomic graphics

Add points to a plotting region, specifically for genomic graphics

circos.genomicPoints(
    region,
    value,
    numeric.column = NULL,
    sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"),
    posTransform = NULL,
    pch = par("pch"),
    col = par("col"),
    cex = par("cex"),
    bg = par("bg"),
    ...)

Arguments

region	A data frame contains 2 columns which correspond to start positions and end positions.
value	A data frame contains values and other information.
numeric.column	Which column in value data frame should be taken as y-value. If it is not defined, the whole numeric columns in value will be taken.
sector.index	Index of sector.
track.index	Index of track.
posTransform	Self-defined function to transform genomic positions, see posTransform.default for explanation
col	Color of points. If there is only one numeric column, the length of col can be either one or number of rows of region. If there are more than one numeric column, the length of col can be either one or number of numeric columns. Pass to circos.points.
pch	Type of points. Settings are similar as col. Pass to circos.points.
cex	Size of points. Settings are similar as col. Pass to circos.points.
bg	Background colors for points.
...	Mysterious parameters.

Details

The function is a low-level graphical function and usually is put in panel.fun when using circos.genomicTrack.

The function behaviours differently from different formats of input, see the examples in the "Examples" Section or go to https://jokergoo.github.io/circlize_book/book/modes-of-input.html for more details.

Examples

circos.par("track.height" = 0.1)
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 100)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})

circos.genomicTrack(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})

bed1 = generateRandomBed(nr = 100)
bed2 = generateRandomBed(nr = 100)
bed_list = list(bed1, bed2)

# data frame list
circos.genomicTrack(bed_list, panel.fun = function(region, value, ...) {
    cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
    i = getI(...)
    circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
})

circos.genomicTrack(bed_list, stack = TRUE,
    panel.fun = function(region, value, ...) {
    cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
    i = getI(...)
    circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})

bed = generateRandomBed(nr = 100, nc = 4)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
    circos.genomicPoints(region, value, cex = 0.5, pch = 16, col = 1:4, ...)
})

circos.genomicTrack(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
    i = getI(...)
    circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})

circos.clear()