Visualize Multi-way Contacts as Hypergraph — geom

Creates a hypergraph visualization for multi-way chromatin contacts where genomic bins are displayed as points (nodes) and reads are shown as vertical lines (hyperedges) connecting multiple bins.

Usage

geom_hypergraph(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  line_width = 0.3,
  line_alpha = 0.6,
  point_size = 2,
  point_alpha = 0.8,
  colour_by = "n_contacts",
  palette = "viridis",
  ...
)

Arguments

mapping: Set of aesthetic mappings created by aes(). Only x, y, and group are used.
data: A data frame from hypergraph_to_tidy().
stat: The statistical transformation to use on the data. Default: "identity".
position: Position adjustment. Default: "identity".
na.rm: If FALSE (default), missing values are removed with a warning.
show.legend: Logical. Should this layer be included in legends?
inherit.aes: If FALSE, overrides the default aesthetics.
line_width: Numeric line width for hyperedges. Default: 0.3.
line_alpha: Numeric transparency for lines. Default: 0.6.
point_size: Numeric size of bin points. Default: 2.
point_alpha: Numeric transparency for points. Default: 0.8.
colour_by: Character: "n_contacts" or "none". Default: "n_contacts".
palette: Character: ggplot2 colour palette. Default: "viridis".
...: Additional arguments passed to layer.

Details

This geom creates a specialized visualization for multi-way chromatin contacts from Pore-C/HiPore-C data. The visualization shows:

Y-axis: Genomic bins (sorted by position)
X-axis: Individual reads (ordered by first appearance)
Lines: Connect all bins contacted by a single read
Points: Individual bin positions
colour: Number of contacts per read (optional)

The visualization is similar to a Sankey diagram but specialized for multi-way genomic interactions.

Aesthetics

geom_hypergraph() understands the following aesthetics: - x (required): Read index or position - y (required): Bin position - group (required): Read identifier - colour (optional): Number of contacts per read

Examples

if (FALSE) { # \dontrun{
# Build hypergraph
hg <- build_hypergraph(
  pairs = pairs_df,
  bin_size = 100000,
  chrom = "chr22",
  quantile = 0.85,
  min_multiway = 3
)

# Convert to tidy format
df <- hypergraph_to_tidy(hg, max_reads = 100)

# Create visualization
ggplot(df, aes(x = read_idx, y = bin, group = read_idx)) +
  geom_hypergraph(aes(colour = n_contacts)) +
  labs(title = "Multi-way Contacts on chr22") +
  theme_minimal()

# Without colouring
ggplot(df, aes(x = read_idx, y = bin, group = read_idx)) +
  geom_hypergraph(colour_by = "none") +
  theme_minimal()
} # }