circlize (version 0.4.1)

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.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"), posTransform = NULL,
    direction = NULL, facing = "inside", niceFacing = FALSE,
    adj = par("adj"), cex = 1, col = "black", font = par("font"), padding = 0,
    extend = 0, ...)

Arguments

region

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

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

Pass to circos.rect

track.index

Pass to circos.rect

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

...

Mysterious parameters

Details

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

References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

Examples

# NOT RUN {
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 20)

circos.genomicTrackPlotRegion(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.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
    circos.genomicText(region, value, labels.column = 2, ...)
})

circos.clear()

# }
# NOT RUN {
# }