R: Create a circle layout

layout_circle {ggbio}

R Documentation

Create a circle layout

Description

Create a circle layout.

Usage

## S4 method for signature 'GRanges'
layout_circle(data, ..., geom = c("point", "line", "link", "ribbon",
                 "rect", "bar", "segment", "hist", "scale", "ideogram",
                 "text"), linked.to, radius = 10, trackWidth = 5,
                 space.skip = 0.015, direction = c("clockwise",
                 "anticlockwise"), link.fun = function(x, y, n = 30)
                 bezier(x, y, evaluation = n), rect.inter.n = 60, rank,
                 scale.n = 60, scale.unit = NULL, scale.type = c("M",
                 "B", "sci"), grid.n = 5, grid.background = "gray70",
                 grid.line = "white", grid = FALSE)

## S4 method for signature 'missing'
layout_circle(data, ...)

Arguments

`data`	A `GRanges` object.
`...`	Extra parameters such as aesthetics mapping in aes(), or `color, size`, etc.
`geom`	The geometric object to use display the data.
`linked.to`	Character indicates column that specifying end of the linking lines, that column should be a `GRanges` object.
`radius`	Numeric value indicates radius. Default is 10.
`trackWidth`	Numeric value indicates the track width.
`space.skip`	Numeric value indicates the ratio of skipped region between chunks(chromosomes in `GRanges`) to the whole track space.
`direction`	Space layout orders.
`link.fun`	Function used for interpolate the linking lines. Default is Hmisc::bezier.
`rect.inter.n`	n passed to interpolate function in rectangle transformation(from a rectangle) to a section in circular view.
`rank`	For default equal trackWidth, use rank to specify the circle orders.
`scale.n`	Approximate number of ticks you want to show on the whole space. used when scale.unit is `NULL`.
`scale.unit`	Unit used for computing scale. Default is `NULL`,
`scale.type`	Scale type used for
`grid`	logical value indicate showing grid background for track or not.
`grid.n`	integer value indicate horizontal grid line number.
`grid.background`	grid background color.
`grid.line`	grid line color.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

N <- 100
library(GenomicRanges)
## ======================================================================
##  simmulated GRanges
## ======================================================================
gr <- GRanges(seqnames = 
              sample(c("chr1", "chr2", "chr3"),
                     size = N, replace = TRUE),
              IRanges(
                      start = sample(1:300, size = N, replace = TRUE),
                      width = sample(70:75, size = N,replace = TRUE)),
              strand = sample(c("+", "-", "*"), size = N, 
                replace = TRUE),
              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
              sample = sample(c("Normal", "Tumor"), 
                size = N, replace = TRUE),
              pair = sample(letters, size = N, 
                replace = TRUE))
seqlengths(gr) <- c(400, 500, 700)
values(gr)$to.gr <- gr[sample(1:length(gr), size = length(gr))]
## doesn't pass gr to the ggplot
ggplot() + layout_circle(gr, geom = "ideo", fill = "gray70", radius = 7, trackWidth = 3) +
  layout_circle(gr, geom = "bar", radius = 10, trackWidth = 4, aes(fill = score, y = score)) +
  layout_circle(gr, geom = "point", color = "red", radius = 14,
                trackWidth = 3, grid = TRUE, aes(y = score)) +
    layout_circle(gr, geom = "link", linked.to = "to.gr", radius = 6,
trackWidth = 1)

plot of chunk unnamed-chunk-1

## more formal API
ggplot(gr) + layout_circle(geom = "ideo", fill = "gray70", radius = 7, trackWidth = 3) +
  layout_circle(geom = "bar", radius = 10, trackWidth = 4, aes(fill = score, y = score)) +
  layout_circle(geom = "point", color = "red", radius = 14,
                trackWidth = 3, grid = TRUE, aes(y = score)) +
    layout_circle(geom = "link", linked.to = "to.gr", radius = 6, trackWidth = 1)

plot of chunk unnamed-chunk-1

[Package ggbio version 1.5.20 ]