circos.genomicRect {circlize}

Draw rectangle-like grid, specifically for genomic graphics

Description

Draw rectangle-like grid, specifically for genomic graphics

Usage

circos.genomicRect(
    region,
    value = NULL,
    ytop = NULL,
    ybottom = NULL,
    ytop.column = NULL,
    ybottom.column = NULL,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    posTransform = NULL,
    col = NA,
    border = "black",
    lty = par("lty"),
    ...)

Arguments

region

A data frame contains 2 column which correspond to start positions and end positions.

value

A data frame contains values and other information.

ytop

A vector or a single value indicating top position of rectangles.

ybottom

A vector or a single value indicating bottom position of rectangles.

ytop.column

If ytop is in value, the index of the column.

ybottom.column

If ybottom is in value, the index of the column.

sector.index

Index of sector.

track.index

Index of track.

posTransform

Self-defined function to transform genomic positions, see posTransform.default for explaination.

col

The length of col can be either one or number of rows of region. Pass to circos.rect.

border

Settings are similar as col. Pass to circos.rect.

lty

Settings are similar as col. Pass to circos.rect.

...

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, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed1 = generateRandomBed(nr = 100)
bed2 = generateRandomBed(nr = 100)
bed_list = list(bed1, bed2)
f = colorRamp2(breaks = c(-1, 0, 1), colors = c("green", "black", "red"))
circos.genomicTrack(bed_list, stack = TRUE,
    panel.fun = function(region, value, ...) {

    circos.genomicRect(region, value, col = f(value[[1]]), 
        border = NA, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})

circos.genomicTrack(bed_list, ylim = c(0, 3),
    panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicRect(region, value, ytop = i+0.4, ybottom = i-0.4, col = f(value[[1]]), 
        border = NA, ...)

    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})

circos.genomicTrack(bed1, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = "red", border = NA, ...)

})

circos.genomicTrack(bed_list, panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicRect(region, value, col = i, border = NA, ...)

})

circos.clear()