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Plot gene structure for one or more genes

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

Draws UTRs, exons, intron chevrons (strand-aware), and optional functional-variant markers for one or more genes. When `facet_rows = FALSE` and more than one gene is requested, a combined- axis facet figure is also written.

Usage

hbr_plot_gene_structure(
  gene_list,
  reference = NULL,
  gff3_path = NULL,
  annotation_source = c("MSU7", "RAPDB", "CUSTOM"),
  cdna_path = NULL,
  cds_path = NULL,
  pep_path = NULL,
  genome_fasta_path = NULL,
  output_dir = NULL,
  figures_dir = "figures",
  n_gene = NULL,
  sort_by = c("Cohens_d", "Superior_Mean"),
  fun_variants = NULL,
  variant_panel_dir = NULL,
  show_variants = TRUE,
  variant_shape_by_region = TRUE,
  aa_full_names = TRUE,
  facet_rows = TRUE,
  palette = "haplobreed",
  theme = "scientific",
  width = 10,
  height = 4,
  formats = c("pdf", "png"),
  combined_pdf = TRUE,
  verbose = TRUE
)

Arguments

gene_list

Gene IDs, path to a summary CSV, directory, or data.frame.

reference

A `hbr_reference` object.

gff3_path

Path to a GFF3 file. Parsed once and cached.

annotation_source

`"MSU7"`, `"RAPDB"`, or `"CUSTOM"`.

cdna_path, cds_path, pep_path, genome_fasta_path

Optional FASTA paths.

output_dir

Directory for figures.

figures_dir

Subdirectory of `output_dir`.

n_gene

Keep at most this many genes.

sort_by

Character vector of columns to rank by.

fun_variants

Optional named list or data.frame.

variant_panel_dir

Directory with per-gene functional SNP files.

show_variants

Draw functional-variant markers.

variant_shape_by_region

Shape by region.

aa_full_names

Expand `R65G` to `Arg65Gly`.

facet_rows

One gene per row or all on a single axis.

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.

verbose

Print progress.

Value

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

Examples

toy <- system.file("extdata", "toy", package = "HaploBreedR")
hbr_plot_gene_structure(
  gene_list         = "gene1",
  gff3_path         = file.path(toy, "toy.gff3"),
  genome_fasta_path = file.path(toy, "toy.fa"),
  output_dir        = tempdir(),
  formats           = "pdf",
  verbose           = FALSE)
#> Loading reference: toy.gff3 / CUSTOM 
#>   GFF3: /home/runner/work/_temp/Library/HaploBreedR/extdata/toy/toy.gff3 
#>   Note: no genome_fasta supplied -- chromosome lengths are approximated from the GFF3's
#>   own maximum feature coordinate per chromosome.
#>   Genes: 1 | Transcripts: 1 | CDS features: 1 | UTR features: 2 
#>   Sequence-resource QC: NO SEQUENCE DATA 
#> Warning: for 'Chr 1  •  1–2 kb (1.5 kb)  •  + strand' in 'mbcsToSbcs': . substituted for • (U+2022)
#> Warning: for 'Chr 1  •  1–2 kb (1.5 kb)  •  + strand' in 'mbcsToSbcs': - substituted for – (U+2013)
#> Warning: for 'Chr 1  •  1–2 kb (1.5 kb)  •  + strand' in 'mbcsToSbcs': . substituted for • (U+2022)