chordDiagram: Plot Chord Diagram

Description

Plot Chord Diagram

Usage

chordDiagram(
    x,
    grid.col = NULL,
    grid.border = NA,
    transparency = 0.5,
    col = NULL,
    row.col = NULL,
    column.col = NULL,
    order = NULL,
    directional = 0,
    xmax = NULL,
    symmetric = FALSE,
    keep.diagonal = FALSE,
    direction.type = "diffHeight",
    diffHeight = mm_h(2),
    link.target.prop = TRUE,
    target.prop.height = mm_h(1),
    reduce = 1e-5,
    self.link = 2,
    preAllocateTracks = NULL,
    annotationTrack = c("name", "grid", "axis"),
    annotationTrackHeight = mm_h(c(3, 2)),
    link.border = NA,
    link.lwd = par("lwd"),
    link.lty = par("lty"),
    link.auto = TRUE,
    link.sort = "default",
    link.decreasing = TRUE,
    link.arr.length = ifelse(link.arr.type == "big.arrow", 0.02, 0.4),
    link.arr.width = link.arr.length/2,
    link.arr.type = "triangle",
    link.arr.lty = par("lty"),
    link.arr.lwd = par("lwd"),
    link.arr.col = par("col"),
    link.largest.ontop = FALSE,
    link.visible = TRUE,
    link.rank = NULL,
    link.zindex = NULL,
    link.overlap = FALSE,
    scale = FALSE,
    group = NULL,
    big.gap = 10,
    small.gap = 1,
    ...)

Value

A data frame which contains positions of links, columns are:

rn: sector name corresponding to rows in the adjacency matrix or the first column in the adjacency list

cn

sector name corresponding to columns in the adjacency matrix or the second column in the adjacency list

value

value for the interaction or relation

o1

order of the link on the "from" sector

o2

order of the link on the "to" sector

x1

and position of the link on the "from" sector, the interval for the link on the "from" sector is c(x1-abs(value), x1)

x2

and position of the link on the "to" sector, the interval for the link on the "from" sector is c(x2-abs(value), x2)

Arguments

x: a matrix or a data frame. The function will pass all argument to chordDiagramFromMatrix or chordDiagramFromDataFrame depending on the type of x, also format of other arguments depends of the type of x. If it is in the form of a matrix, it should be an adjacency matrix. If it is in the form of a data frame, it should be an adjacency list.
grid.col: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
grid.border: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
transparency: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
col: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
row.col: pass to chordDiagramFromMatrix
column.col: pass to chordDiagramFromMatrix
order: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
directional: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
xmax: maximum value on x-axes, the value should be a named vector.
symmetric: pass to chordDiagramFromMatrix
keep.diagonal: pass to chordDiagramFromMatrix
direction.type: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
diffHeight: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.target.prop: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
target.prop.height: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
reduce: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
self.link: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
preAllocateTracks: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
annotationTrack: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
annotationTrackHeight: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.border: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.lwd: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.lty: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.auto: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.sort: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.decreasing: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.arr.length: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.arr.width: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.arr.type: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.arr.lty: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.arr.lwd: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.arr.col: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.largest.ontop: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.visible: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.rank: This is argument is removed.
link.zindex: order to add links to the circle, a large value means to add it later.
link.overlap: pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
scale: scale each sector to same width
group: It contains the group labels and the sector names are used as the names in the vector.
big.gap: Gap between the two sets of sectors. If the input is a matrix, the two sets are row sectors and column sectors. If the input is a data frame, the two sets correspond to the first column and the second column. It only works when there is no intersection between the two sets.
small.gap: Small gap between sectors.
...: pass to circos.link.

Details

Chord diagram is a way to visualize numeric tables ( http://circos.ca/intro/tabular_visualization/ ), especially useful when the table represents information of directional relations. This function visualize tables in a circular way.

This function is flexible and contains some settings that may be a little difficult to understand. Please refer to vignette for better explanation.

Examples

Run this code

set.seed(999)
mat = matrix(sample(18, 18), 3, 6)
rownames(mat) = paste0("S", 1:3)
colnames(mat) = paste0("E", 1:6)

df = data.frame(from = rep(rownames(mat), times = ncol(mat)),
    to = rep(colnames(mat), each = nrow(mat)),
    value = as.vector(mat),
    stringsAsFactors = FALSE)

chordDiagram(mat)
chordDiagram(df)
circos.clear()