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Plot a haplotype network for one or more genes

Source: R/plot-functions.r
hbr_plot_haplotype_network.Rd

Renders a minimal spanning graph of a gene's haplotypes: nodes sized by frequency, edges drawn when two haplotypes differ by exactly one SNP. Optionally highlights and labels the superior haplotype.

Usage

hbr_plot_haplotype_network(
  gene_list,
  output_dir = NULL,
  summary_csv = NULL,
  per_gene_dir = NULL,
  result = NULL,
  reference = NULL,
  gff3_path = NULL,
  trait_col = "NT",
  n_gene = NULL,
  sort_by = c("Cohens_d", "Superior_Mean"),
  colour_by_superior = TRUE,
  label_superior = TRUE,
  layout = c("circle", "grid"),
  node_scale = 1,
  palette = "haplobreed",
  theme = "haplobreed",
  width = 8,
  height = 7,
  formats = c("pdf", "png"),
  combined_pdf = TRUE,
  figures_dir = "figures",
  verbose = TRUE
)

Arguments

gene_list

IDs, CSV path, directory path, or data.frame.

output_dir

Directory holding per-gene files.

summary_csv

Optional path to the summary CSV.

per_gene_dir

Override for the directory holding per-gene files.

result

Optional in-memory [haplobreed_analysis()] output.

reference

Optional `hbr_reference` object.

gff3_path

Optional GFF3 path; parsed once and cached for the session.

trait_col

Trait column name.

n_gene

Keep at most this many genes.

sort_by

Character vector of columns to rank by.

colour_by_superior

Highlight the superior node.

label_superior

Label the superior node.

layout

`"circle"` or `"grid"`.

node_scale

Multiplier for maximum node radius.

palette

One of [hbr_palette_names()].

theme

One of [hbr_theme_names()].

width, height

Figure dimensions in inches.

formats

Output formats.

combined_pdf

Also write a multi-page PDF.

figures_dir

Subdirectory of `output_dir` for figures.

verbose

Print progress.

Value

Invisibly, a list with `plots`, `files`, `missing_genes`, `combined_pdf`.

Examples

toy <- system.file("extdata", "toy", package = "HaploBreedR")
hbr_plot_haplotype_network(
  gene_list    = "gene1",
  output_dir   = tempdir(),
  per_gene_dir = toy,
  trait_col    = "trait_value",
  formats      = "pdf",
  combined_pdf = FALSE,
  verbose      = FALSE)
#> Warning: for '2 haplotypes • superior = Hap1' in 'mbcsToSbcs': . substituted for • (U+2022)
#> Warning: for 'gene1 — haplotype network' in 'mbcsToSbcs': - substituted for — (U+2014)