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

In 1156054203/circlize-: Circular Visualization

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()


## End(Not run)

1156054203/circlize- documentation built on May 22, 2019, 2 p.m.