circlizePlus (version 0.9.0)

ccTrack: Define a generic track

Description

Object ccTrack will call the function circlize::circos.trackPlotRegion while drawing.

Usage

ccTrack(
  sectors = NULL,
  x = NULL,
  y = NULL,
  ylim = NULL,
  force.ylim = TRUE,
  track.index = NULL,
  track.height = circos.par("track.height"),
  track.margin = circos.par("track.margin"),
  cell.padding = circos.par("cell.padding"),
  bg.col = NA,
  bg.border = "black",
  bg.lty = par("lty"),
  bg.lwd = par("lwd"),
  panel.fun = function(x, y) {
     NULL
 },
  factors = sectors
)

Value

Object ccTrack

Arguments

sectors

A factor or a character vector which represents categories of data, if it is NULL, then it uses all sector index.

x

Data on x-axis. It is only used if panel.fun is set.

y

Data on y-axis

ylim

Range of data on y-axis

force.ylim

Whether to force all cells in the track to share the same ylim. Normally, all cells on a same track should have same ylim.

track.index

Index for the track which is going to be created/updated. If the specified track has already been created, this function just updated corresponding track with new plot. If the specified track is NULL or has not been created, this function just creates it. Note the value for this argument should not exceed maximum track index plus 1.

track.height

Height of the track. It is the percentage to the radius of the unit circles. The value can be set by uh to an absolute unit. If updating a track (with proper track.index value), this argument is ignored.

track.margin

only affect current track

cell.padding

only affect current track

bg.col

Background color for the plotting regions. It can be vector which has the same length of sectors.

bg.border

Color for the border of the plotting regions. It can be vector which has the same length of sectors.

bg.lty

Line style for the border of the plotting regions. It can be vector which has the same length of sectors.

bg.lwd

Line width for the border of the plotting regions. It can be vector which has the same length of sectors.

panel.fun

Panel function to add graphics in each cell, see "details" section and vignette for explanation.

factors

The same as sectors. It will be removed in future versions.

Examples

library(circlizePlus)
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
par1=ccPar("track.height" = 0.1)
cc=ccPlot(sectors = df$sectors, x = df$x) + par1
track1 = ccTrack(sectors = df$sectors, y = df$y,
                 panel.fun = function(x, y) {
                   circos.text(CELL_META$xcenter,
                               CELL_META$cell.ylim[2] + mm_y(5),
                               CELL_META$sector.index)
                   circos.axis(labels.cex = 0.6)
                 })
cc=cc+track1
cc
circos.clear()