Skip to contents

Plot gene structure (Promoter, 3'UTR, Exon, Intron, 5'UTR)

Source: R/plot_gene_structure.R
plot_gene_structure.Rd

Plot gene structure (Promoter, 3'UTR, Exon, Intron, 5'UTR).

Usage

plot_gene_structure(
  gff_file,
  format = "auto",
  gene_id,
  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").

gene_id

Gene id same as GFF3/GTF. (necessary).

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 gene structure.

Author

benben-miao

Examples

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

# Plot gene structure
plot_gene_structure(
  gff_file = gff_file,
  format = "auto",
  gene_id = "ENSMUSG00000025935",
  upstream = 2000,
  downstream = 200,
  feature_alpha = 0.8,
  intron_width = 1,
  x_breaks = 10,
  arrow_length = 5,
  arrow_count = 1,
  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