circos.genomicText {circlize}

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()