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Plot chromosome structures and gene stats

Source: R/plot_chrom_structure.R
plot_chrom_structure.Rd

Plot chromosome structures and gene stats.

Usage

plot_chrom_structure(
  gff_file,
  format = "auto",
  orientation = "vertical",
  bar_width = 0.6,
  chrom_alpha = 0.1,
  gene_width = 0.5,
  chrom_color = "#008888",
  gene_color = "#0088ff",
  telomere_color = "#ff0000",
  label_size = 3
)

Arguments

gff_file

Genomic structural annotation GFF3/GTF file path.

format

Format of GFF3/GTF file. ("auto", "gff3", "gtf").

orientation

Coordinate orientation: ("vertical", "horizontal").

bar_width

Chromosome bars relative width. (0.6).

chrom_alpha

Chromosome bars alpha. (0.2).

gene_width

Gene bar relative width. (0.5).

chrom_color

Chromosome bar color. ("#008888").

gene_color

Gene rectangle color. ("#0088ff").

telomere_color

Telomere color. ("#ff0000").

label_size

Label text size. (3).

Value

Plot of chromosome structure.

Examples

# Example GFF3 file in GAnnoViz
gff_file <- system.file(
  "extdata",
  "example.gff3.gz",
  package = "GAnnoViz")

plot_chrom_structure(
  gff_file = gff_file,
  format = "auto",
  orientation = "vertical",
  bar_width = 0.6,
  chrom_alpha = 0.1,
  gene_width = 0.5,
  chrom_color = "#008888",
  gene_color = "#0088ff",
  telomere_color = "#ff0000",
  label_size = 3
)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK