chordDiagram {circlize}R Documentation

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,
    symmetric = FALSE, keep.diagonal = FALSE,
    direction.type = "diffHeight", diffHeight = convert_height(2, "mm"),
    reduce = 1e-5, self.link = 2,
    preAllocateTracks = NULL,
    annotationTrack = c("name", "grid", "axis"),
    annotationTrackHeight = convert_height(c(3, 2), "mm"),
    link.border = NA, link.lwd = par("lwd"), link.lty = par("lty"),
    link.sort = FALSE, 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, ...)

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

symmetric

pass to chordDiagramFromMatrix

keep.diagonal

pass to chordDiagramFromMatrix

direction.type

pass to chordDiagramFromMatrix or chordDiagramFromDataFrame

diffHeight

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.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

order to add links to the circle, a large value means to add it later.

...

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.

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)

References

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

See Also

http://jokergoo.github.io/circlize_book/book/the-chorddiagram-function.html

Examples

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()
[Package circlize version 0.4.1 Index]