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Chord / Circos plot

Source: R/chordplot.R
chordplot.Rd

Draws a chord diagram (also known as a circos plot) to visualise relationships between two categorical variables. Categories are arranged around a circle, and connecting ribbons (links) represent the flow or association between source and target nodes. The width of each link is proportional to the associated numeric value or observation count.

The function supports count aggregation (omit y to plot observation counts per pair), link colouring by source or target node, label rotation options, and splitting into separate sub-diagrams via split_by.

CircosPlot is an alias of ChordPlot.

CircosPlot is an alias for ChordPlot.

Usage

ChordPlot(
  data,
  y = NULL,
  from = NULL,
  from_sep = "_",
  to = NULL,
  to_sep = "_",
  split_by = NULL,
  split_by_sep = "_",
  flip = FALSE,
  links_color = c("from", "to"),
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 0.5,
  labels_rot = FALSE,
  title = NULL,
  subtitle = NULL,
  seed = 8525,
  keep_na = FALSE,
  keep_empty = FALSE,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

CircosPlot(
  data,
  y = NULL,
  from = NULL,
  from_sep = "_",
  to = NULL,
  to_sep = "_",
  split_by = NULL,
  split_by_sep = "_",
  flip = FALSE,
  links_color = c("from", "to"),
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 0.5,
  labels_rot = FALSE,
  title = NULL,
  subtitle = NULL,
  seed = 8525,
  keep_na = FALSE,
  keep_empty = FALSE,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

data

A data frame.

y

A character string specifying the column name of the data frame to plot for the y-axis.

from

A character string (or vector) specifying the column name(s) for the source nodes. Character/factor columns are expected. Multiple columns are concatenated with from_sep.

from_sep

A character string to join multiple from columns. Default "_".

to

A character string (or vector) specifying the column name(s) for the target nodes. Character/factor columns are expected. Multiple columns are concatenated with to_sep.

to_sep

A character string to join multiple to columns. Default "_".

split_by

The column(s) to split the data by for separate sub-diagrams. Multiple columns are concatenated with split_by_sep.

split_by_sep

A character string to separate concatenated split_by columns. Default "_".

flip

Logical; if TRUE, swap the source and target nodes, reversing the link direction.

A character string controlling which node's colour each link ribbon takes: "from" (default) or "to".

theme

A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".

theme_args

A list of arguments to pass to the theme function.

palette

A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.

palcolor

A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).

palreverse

A logical value indicating whether to reverse the palette. Default is FALSE.

alpha

A numeric value specifying the transparency of the plot.

labels_rot

Logical; if TRUE, rotate sector labels by 90 degrees (clockwise). Default FALSE uses niceFacing for automatic orientation.

title

A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.

subtitle

A character string specifying the subtitle of the plot.

seed

A numeric seed for reproducibility.

keep_na

A logical value or a character to replace the NA values in the data. It can also take a named list to specify different behavior for different columns. If TRUE or NA, NA values will be replaced with NA. If FALSE, NA values will be removed from the data before plotting. If a character string is provided, NA values will be replaced with the provided string. If a named vector/list is provided, the names should be the column names to apply the behavior to, and the values should be one of TRUE, FALSE, or a character string. Without a named vector/list, the behavior applies to categorical/character columns used on the plot, for example, the x, group_by, fill_by, etc.

keep_empty

One of FALSE, TRUE and "level". It can also take a named list to specify different behavior for different columns. Without a named list, the behavior applies to the categorical/character columns used on the plot, for example, the x, group_by, fill_by, etc.

  • FALSE (default): Drop empty factor levels from the data before plotting.

  • TRUE: Keep empty factor levels and show them as a separate category in the plot.

  • "level": Keep empty factor levels, but do not show them in the plot. But they will be assigned colors from the palette to maintain consistency across multiple plots. Alias: levels

combine

Logical; when TRUE (default), returns a combined patchwork object. When FALSE, returns a named list of individual wrapped elements.

ncol, nrow

Integer number of columns / rows for the combined layout.

byrow

Logical; fill the combined layout by row (default TRUE).

axes, axis_titles

Character strings for axis handling in the combined layout.

guides

Character string for legend collection across panels.

design

A custom layout design for the combined plot.

...

Additional arguments.

Value

A patchwork object or a named list of wrapped elements (when combine = FALSE), each with height and width attributes in inches.

split_by workflow

When split_by is provided:

  1. check_keep_na() and check_keep_empty() normalise the keep_na / keep_empty arguments for all columns (split_by, from, to).

  2. The split_by column is validated and its NA / empty levels are processed. It is then removed from the per-column lists.

  3. The data is split by split_by (preserving level order). If split_by is NULL, the data is wrapped in a single-element list with name "...".

  4. Per-split palette and palcolor are resolved via check_palette() and check_palcolor().

  5. ChordPlotAtomic() is called for each split. When title is a function, it receives the split level name for dynamic titles.

  6. Results are combined via combine_plots().

Examples

# \donttest{
set.seed(8525)
data <- data.frame(
    nodes1 = sample(c("Soure1", "Source2", "Source3"), 10, replace = TRUE),
    nodes2 = sample(letters[1:3], 10, replace = TRUE),
    y = sample(1:5, 10, replace = TRUE)
)

# Basic chord diagram (counts)
ChordPlot(data, from = "nodes1", to = "nodes2")


# Links coloured by target + rotated labels
ChordPlot(data, from = "nodes1", to = "nodes2",
          links_color = "to", labels_rot = TRUE)


# With explicit y values (link thickness)
ChordPlot(data, from = "nodes1", to = "nodes2", y = "y")


# Split by a column — one diagram per split level
ChordPlot(data, from = "nodes1", to = "nodes2", split_by = "y")


# Per-split palettes
ChordPlot(data, from = "nodes1", to = "nodes2", split_by = "y",
          palette = c("1" = "Reds", "2" = "Blues",
                      "3" = "Greens", "4" = "Purp"))


# Flip source/target direction
ChordPlot(data, from = "nodes1", to = "nodes2", flip = TRUE)

# }