circos.trackPlotRegion: Create plotting regions for a whole track

Description Usage Arguments Details Panel References See Also Examples

View source: R/plot.R

Description

Create plotting regions for a whole track

Usage

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circos.trackPlotRegion(factors = 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})

Arguments

factors

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.

Details

This function tends to be a high-level plotting function, which means, you must first call this function to create plotting regions, then those low-level graphic function such as circos.points, circos.lines can be applied.

Currently, all the cells that are created in a same track sharing same height, which means, there is no cell has larger height than others.

Since ranges for values on x-axis has already been defined by circos.initialize, only ranges for values on y-axis should be specified in this function. There are two ways to identify the ranges for values on y-axes either by y or ylim. If y is set, it must has the same length as factors and the ylim for each cell is calculated from y values. Also, the ylim can be specified from ylim which can be a two-element vector or a matrix which has two columns and the number of rows is the same as the length of the levels of the factors.

If there is no enough space for the new track or the new track overlaps with other tracks, there will be an error.

If factors does not cover all sectors, the cells in remaining unselected sectors would also be created but without drawing anything. The ylim for these cells are the same as that in the last created cell.

The function can also update a already-created track if the index for the track is specified. If updating an existed track, those parameters related to the position (such as track height and track margin) of the plotting region can not be changed.

Panel

panel.fun provides a convenient way to add graphics in each cell when initializing the tracks. The self-defined function needs two arguments: x and y which correspond to the data points in the current cell. When factors, x, and y are set in circos.trackPlotRegion, a subset of x and y are split by factors and are sent to panel.fun in the "current" cell. circos.trackPlotRegion creates plotting regions one by one on the track and panel.fun adds graphics in the 'current' cell after the plotting region for a certain cell has been created.

See vignette for examples of how to use this feature.

References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

See Also

http://jokergoo.github.io/circlize_book/book/circular-layout.html

Examples

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circos.initialize(letters[1:8], xlim = c(0, 1))
set.seed(123)
df = data.frame(fa = sample(letters[1:8], 100, replace = TRUE),
                x = runif(100), y = rnorm(100))
circos.track(ylim = c(0, 1), bg.col = rand_color(8))
circos.track(df$fa, x = df$x, y = df$y, panel.fun = function(x, y) {
    circos.points(x, y)
}, track.height = 0.2, bg.border = rand_color(8))
circos.clear()

jokergoo/circlize documentation built on Aug. 11, 2019, 11:01 a.m.