Skip to contents

Plot a Minimum-Spanning Haplotype Network for One LD Block

Source: R/haplotype_analysis.R
plot_haplotype_network.Rd

Draws a minimum-spanning network (MSN) of haplotype alleles within a single LD block using igraph. Nodes represent alleles; edge weights are Hamming distances (number of differing SNP positions). Node size is proportional to allele frequency. Optional colour by population or phenotypic group.

Usage

plot_haplotype_network(
  haplotypes,
  block_id,
  groups = NULL,
  min_freq = 0.02,
  missing_string = ".",
  title = NULL,
  palette = NULL
)

Arguments

haplotypes

Named list from extract_haplotypes.

block_id

Character. Name of the block to visualise (must be in names(haplotypes)).

groups

Named character vector mapping individual IDs to group labels (used for node pie-chart colouring). NULL = all one colour.

min_freq

Numeric. Alleles below this frequency are dropped before plotting. Default 0.02.

missing_string

Character. Missing haplotype placeholder. Default ".".

title

Character. Plot title. Default = block_id.

palette

Character vector of colours for groups. NULL uses a built-in palette.

Value

Invisibly returns the igraph graph object. The network is plotted as a side effect.

See also

extract_haplotypes, compute_haplotype_diversity

Examples

# \donttest{
data(ldx_geno, ldx_snp_info, ldx_blocks, package = "LDxBlocks")
haps <- extract_haplotypes(ldx_geno, ldx_snp_info, ldx_blocks)
plot_haplotype_network(haps, block_id = names(haps)[1])

# }