circlize: circos.genomicText – R documentation

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circos.genomicText

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

Circular Visualization

v0.4.12

MIT + file LICENSE

Authors

Zuguang Gu

Initial release

2021-1-8

circos.genomicText

Description

Usage

Arguments

Details

Examples

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