circos.genomicText: Draw text in a cell, specifically for genomic graphics

In circlize: Circular Visualization

Draw text in a cell, specifically for genomic graphics

Description

Draw text in a cell, specifically for genomic graphics

Usage

circos.genomicText(
    region,
    value = NULL,
    y = NULL,
    labels = NULL,
    labels.column = NULL,
    numeric.column = NULL,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    posTransform = NULL,
    direction = NULL,
    facing = "inside",
    niceFacing = FALSE,
    adj = par("adj"),
    cex = 1,
    col = "black",
    font = par("font"),
    padding = 0,
    extend = 0,
    align_to = "region",
    ...)

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.
y	A vector or a single value indicating position of text.
labels	Labels of text corresponding to each genomic positions.
labels.column	If labels are in value, index of column in value.
numeric.column	Which column in value data frame should be taken as y-value. If it is not defined, only the first 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.
facing	Passing to circos.text. Settings are similar as col.
niceFacing	Should the facing of text be adjusted to fit human eyes?
direction	Deprecated, use facing instead.
adj	Pass to circos.text. Settings are similar as col.
cex	Pass to circos.text. Settings are similar as col.
col	Pass to circos.text. The length of col can be either one or number of rows of region.
font	Pass to circos.text. Settings are similar as col.
padding	pass to posTransform if it is set as posTransform.text.
extend	pass to posTransform if it is set as posTransform.text.
align_to	pass to posTransform if it is set as posTransform.text.
...	Mysterious parameters.

Details

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

Examples

circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 20)

circos.genomicTrack(bed, ylim = c(0, 1), panel.fun = function(region, value, ...) {
    circos.genomicText(region, value, y = 0.5, labels = "text", ...)
})

bed = cbind(bed, sample(letters, nrow(bed), replace = TRUE))
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicText(region, value, labels.column = 2, ...)
})

circos.clear()

circlize documentation built on May 29, 2024, 1:59 a.m.