Draws a two-panel figure: a haplotype boxplot (with jittered points, mean +/- SE overlay, and post-hoc letters) and a haplotype summary table (N, frequency, per-SNP alleles, mean/SE, superior marker). The function has two modes: **pipeline mode** (supply `gene_id` + `hap_data` + `test_res`) and **CSV mode** (supply `gene_csv` or `gene_data` + optional individuals/genotype files).
Usage
hbr_plot_haplotype(
gene_id = NULL,
hap_data = NULL,
test_res = NULL,
trait_col = "trait",
output_dir = NULL,
superior_info = NULL,
functional_snps_used = NULL,
adjusted_p = NA_real_,
aa_full_names = TRUE,
formats = c("pdf", "tiff", "png"),
gene_list = NULL,
gene_data = NULL,
individuals_csv = NULL,
individuals_data = NULL,
geno_file = NULL,
geno_matrix = NULL,
geno_format = NULL,
plink_path = "plink",
gene_csv = NULL
)Arguments
- gene_id
Gene ID (pipeline mode).
- hap_data
Test objects from the pipeline (pipeline mode).
- test_res
Test results from the pipeline (pipeline mode).
- trait_col
Trait column name.
- output_dir
Output directory. `NULL` writes to the working directory.
- superior_info
Superior-haplotype info (pipeline mode).
- functional_snps_used
SNPs used (pipeline mode).
- adjusted_p
Optional FDR-adjusted p-value.
- aa_full_names
Use three-letter amino-acid codes.
- formats
Output formats. Any of `"pdf"`, `"png"`, `"tiff"`, `"svg"`.
- gene_list
Alternative: gene ID (CSV mode).
- gene_data, gene_csv
Alternative: in-memory or CSV input (CSV mode).
- individuals_csv, individuals_data
Alternative individuals source (CSV mode).
- geno_file, geno_matrix, geno_format
Alternative genotype source (CSV mode).
- plink_path
Path to PLINK.
Examples
toy <- system.file("extdata", "toy", package = "HaploBreedR")
hbr_plot_haplotype(
gene_list = "gene1",
gene_csv = file.path(toy, "gene1_viz.csv"),
individuals_csv = file.path(toy, "gene1_individuals.csv"),
trait_col = "trait_value",
output_dir = tempdir(),
formats = "pdf")
#> Warning: for 'gene1 — haplotype summary' in 'mbcsToSbcs': - substituted for — (U+2014)