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Plot gene structures for a genomic interval

Source: R/plot_interval_structure.R
plot_interval_structure.Rd

Plot gene structures for a genomic interval.

Usage

plot_interval_structure(
  gff_file,
  format = "auto",
  chrom_id,
  start,
  end,
  x_breaks = 10,
  upstream = 2000,
  downstream = 200,
  feature_alpha = 0.8,
  intron_width = 1,
  arrow_count = 1,
  arrow_length = 5,
  arrow_unit = "pt",
  promoter_color = "#ff8800",
  utr5_color = "#008833",
  utr3_color = "#ff0033",
  exon_color = "#0033ff",
  intron_color = "#333333"
)

Arguments

gff_file

Genomic structural annotation GFF3/GTF file path.

format

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

chrom_id

Chromosome id (must match the annotation).

start

Window start coordinate (bp, genomic absolute coordinate).

end

Window end coordinate (bp, genomic absolute coordinate).

x_breaks

X axis breaks number. (10).

upstream

Promoter upstream (bp). (2000).

downstream

Promoter downstream (bp). (200).

feature_alpha

Elements alpha. (0.8).

intron_width

Intron line width. (1).

arrow_count

Intron arrow number bold. (1).

arrow_length

Intron arrows length（pt). (1).

arrow_unit

Intron arrow length unit. ("pt", "mm").

promoter_color

Promoter color. ("#ff8800").

utr5_color

5'UTR color. ("#008833").

utr3_color

3'UTR color. ("#ff0033").

exon_color

Exon color. ("#0033ff").

intron_color

Intron color. ("#333333").

Value

Plot of genomic interval structure.

Examples

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

plot_interval_structure(
  gff_file = gff_file,
  format = "auto",
  chrom_id = "chr1",
  start = 13600000,
  end = 13800000,
  x_breaks = 10,
  upstream = 2000,
  downstream = 200,
  feature_alpha = 0.8,
  intron_width = 1,
  arrow_count = 1,
  arrow_length = 5,
  arrow_unit = "pt",
  promoter_color = "#ff8800",
  utr5_color = "#008833",
  utr3_color = "#ff0033",
  exon_color = "#0033ff",
  intron_color = "#333333"
)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK