Add labels to specified genomic regions

Add labels to specified genomic regions

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"),
    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	Aize 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.

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

# \donttest{
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()
# }