R: Add labels to specified genomic regions

circos.genomicLabels {circlize} | R Documentation

## Add labels to specified genomic regions

### Description

Add labels to specified genomic regions

### Usage

    circos.genomicLabels(bed, labels = NULL, labels.column = NULL,
        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`
`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.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### 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]])))

    ## End(Not run)

[Package circlize version 0.4.5 Index]