circos.genomicLabels {circlize}

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 = mm_h(5),
    line_col = par("col"),
    line_lwd = par("lwd"),
    line_lty = par("lty"),
    labels_height = min(c(cm_h(1.5), max(strwidth(labels, cex = cex, font = font)))),
    side = c("inside", "outside"),
    labels.side = side,
    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

fFacing 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?

labels.side

Same as side. It will replace side in the future versions.

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.

This function creates two tracks, one for the connection lines and one for the labels.

See Also

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

Examples

circos.initializeWithIdeogram()
bed = generateRandomBed(nr = 50, fun = function(k) sample(letters, k, replace = TRUE))
bed[1, 4] = "aaaaa"
circos.genomicLabels(bed, labels.column = 4, side = "inside")
circos.clear()

circos.initializeWithIdeogram(plotType = NULL)
circos.genomicLabels(bed, labels.column = 4, side = "outside",
    col = as.numeric(factor(bed[[1]])), line_col = as.numeric(factor(bed[[1]])))
circos.genomicIdeogram()
circos.clear()