chordDiagram | R Documentation |

Plot Chord Diagram

```
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,
...)
```

`x` |
a matrix or a data frame. The function will pass all argument to |

`grid.col` |
pass to |

`grid.border` |
pass to |

`transparency` |
pass to |

`col` |
pass to |

`row.col` |
pass to |

`column.col` |
pass to |

`order` |
pass to |

`directional` |
pass to |

`xmax` |
maximum value on x-axes, the value should be a named vector. |

`symmetric` |
pass to |

`keep.diagonal` |
pass to |

`direction.type` |
pass to |

`diffHeight` |
pass to |

`link.target.prop` |
pass to |

`target.prop.height` |
pass to |

`reduce` |
pass to |

`self.link` |
pass to |

`preAllocateTracks` |
pass to |

`annotationTrack` |
pass to |

`annotationTrackHeight` |
pass to |

`link.border` |
pass to |

`link.lwd` |
pass to |

`link.lty` |
pass to |

`link.auto` |
pass to |

`link.sort` |
pass to |

`link.decreasing` |
pass to |

`link.arr.length` |
pass to |

`link.arr.width` |
pass to |

`link.arr.type` |
pass to |

`link.arr.lty` |
pass to |

`link.arr.lwd` |
pass to |

`link.arr.col` |
pass to |

`link.largest.ontop` |
pass to |

`link.visible` |
pass to |

`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 |

`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 |

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.

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)`

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

```
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()
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.