chordDiagram: Plot Chord Diagram

In 1156054203/circlize-: Circular Visualization

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 = 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, scale = FALSE, ...)

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
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.
scale	scale each sector to same width
...	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()

1156054203/circlize- documentation built on May 22, 2019, 2 p.m.