Add text for genomic data visualization — ccGenomicText • circlizePlus

Object ccGenomicCellGeom will call the function circlize::circos.genomicText while drawing.

Usage

ccGenomicText(...)

Arguments

...

Arguments passed on to circlize::circos.genomicText

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.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
cc = ccPlot(initMode="initializeWithIdeogram",plotType = NULL)
bed = generateRandomBed(nr = 20)
track1 = ccGenomicTrack(data=bed, ylim = c(0, 1))
all_chr = c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY")
text1 = ccGenomicText(y = 0.5, labels = "text")
cells1 = ccCells(sector.indexes = all_chr) + text1
cc + (track1 + cells1)