circos.genomicPoints {circlize}

Add points to a plotting region, specifically for genomic graphics

Description

Add points to a plotting region, specifically for genomic graphics

Usage

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()