circos.genomicLines {circlize}

Add lines to a plotting region, specifically for genomic graphics

Description

Add lines to a plotting region, specifically for genomic graphics

Usage

circos.genomicLines(
    region,
    value,
    numeric.column = NULL,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    posTransform = NULL,
    col = ifelse(area, "grey", "black"),
    lwd = par("lwd"),
    lty = par("lty"),
    type = "l",
    area = FALSE,
    area.baseline = NULL,
    border = "black",
    baseline = "bottom",
    pt.col = par("col"),
    cex = par("cex"),
    pch = par("pch"),
    ...)

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.

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 explaination.

col

col of lines/areas. If there are more than one numeric column, the length of col can be either one or number of numeric columns. If there is only one numeric column and type is either segment or h, the length of col can be either one or number of rows of region. pass to circos.lines

lwd

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

lty

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

type

There is an additional option segment which plot segment lines from start position to end position. Settings are similar as col. Pass to circos.lines.

area

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

area.baseline

Deprecated, use baseline instead.

baseline

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

border

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

pt.col

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

cex

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

pch

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

...

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

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

bed = generateRandomBed(nr = 100)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicLines(region, value, type = "l", ...)
})

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

circos.genomicTrack(bed_list, panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicLines(region, value, col = i, ...)
})

circos.genomicTrack(bed_list, stack = TRUE, 
    panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicLines(region, value, col = i, ...)
})

bed = generateRandomBed(nr = 100, nc = 4)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicLines(region, value, col = 1:4, ...)
})

circos.genomicTrack(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicLines(region, value, col = i, ...)
})

bed = generateRandomBed(nr = 100)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicLines(region, value, type = "segment", lwd = 2, ...)
})

circos.clear()