Add labels to specific genomic track — ccGenomicLabels • circlizePlus

Object ccGenomicTrack will call the function circlize::circos.genomicLabels while drawing.

Usage

ccGenomicLabels(
  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.

Value

Object ccGenomicTrack

Examples

library(circlizePlus)
bed = generateRandomBed(nr = 50, fun = function(k) sample(letters, k, replace = TRUE))
bed[1, 4] = "aaaaa"
cc = ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
t1 = ccGenomicLabels(bed, labels.column = 4, side = "outside",
                     col = as.numeric(factor(bed[[1]])), line_col = as.numeric(factor(bed[[1]])))
#> Warning: `convert_length()` only works when aspect of the coordinate is 1.
#> Warning: `convert_length()` only works when aspect of the coordinate is 1.
#> Error in strwidth(labels, cex = cex, font = font): plot.new has not been called yet
cc + t1
#> Error: object 't1' not found
circos.clear()