circlize (version 0.4.10)

circos.genomicLabels: Add labels to specified genomic regions

Description

Add labels to specified genomic regions

Usage

circos.genomicLabels(
    bed,
    labels = NULL,
    labels.column = NULL,
    facing = "clockwise",
    niceFacing = TRUE,
    col = par("col"),
    cex = 0.8,
    font = par("font"),
    padding = 0.4,
    connection_height = convert_height(5, "mm"),
    line_col = par("col"),
    line_lwd = par("lwd"),
    line_lty = par("lty"),
    labels_height = min(c(convert_height(1.5, "cm"),
    max(strwidth(labels, cex = cex, font = font)))),
    side = c("inside", "outside"),
    track.margin = circos.par("track.margin"))

Arguments

bed

a data frame in bed format

labels

a vector of labels corresponding to rows in bed

labels.column

if the label column is already in bed, the index for this column in bed

facing

facing of the labels. The value can only be 'clockwise' or 'reverse.clockwise'.

niceFacing

whether automatically adjust the facing of the labels.

col

color for the labels

cex

size of the labels

font

font of the labels

padding

padding of the labels, the value is the ratio to the height of the label

connection_height

height of the connection track

line_col

color for the connection lines

line_lwd

line width for the connection lines

line_lty

line type for the connectioin lines

labels_height

height of the labels track

side

side of the labels track, is it in the inside of the track where the regions are marked?

track.margin

bottom and top margins

Details

The function adds labels for the specified regions. The positions of labels are arranged so that they are not overlapping to each other.

See Also

https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#labels

Examples

# NOT RUN {
circos.initializeWithIdeogram(plotType = c("labels", "axis"))
bed = generateRandomBed(nr = 100, fun = function(k) sample(letters, k, replace = TRUE))
bed[1, 4] = "aaaaaaaa"
circos.genomicLabels(bed, labels.column = 4, side = "inside",
    col = as.numeric(factor(bed[[1]])))
circos.genomicLabels(bed, labels.column = 4, side = "outside",
    line_col = as.numeric(factor(bed[[1]])))
# }