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Gene neighborhood architecture around a focal gene

Source: R/plot_interval_flank.R
plot_interval_flank.Rd

Plot gene neighborhood around a focal gene with distances, arrows for strand, and optional promoter track.

Usage

plot_interval_flank(
  gff_file,
  format = "auto",
  gene_id,
  flank_upstream = 2e+05,
  flank_downstream = 2e+05,
  show_promoters = TRUE,
  upstream = 2000,
  downstream = 200,
  arrow_length = 5,
  arrow_unit = "pt",
  gene_color = "#0088ff",
  promoter_color = "#ff8800",
  label_size = 3
)

Arguments

gff_file

Genomic structural annotation GFF3/GTF file path.

format

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

gene_id

Focal gene id consistent with GFF/GTF. (necessary).

flank_upstream

Upstream flank window (bp). (200000).

flank_downstream

Downstream flank window (bp). (200000).

show_promoters

Whether to draw a promoter track. (TRUE).

upstream

Promoter upstream (bp). (2000).

downstream

Promoter downstream (bp). (200).

arrow_length

Length of strand arrows (pt). (5).

arrow_unit

Arrow length unit. ("pt", "mm").

gene_color

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

promoter_color

Promoter bar color. ("#ff8800").

label_size

Label text size. (3).

Value

A ggplot object of genes within a flank window around the focal gene.

Author

benben-miao

Examples

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

# Neighborhood around a focal gene on its chromosome
plot_interval_flank(
  gff_file = gff_file,
  format = "auto",
  gene_id = "ENSMUSG00000025935",
  flank_upstream = 200000,
  flank_downstream = 200000,
  show_promoters = TRUE,
  upstream = 2000,
  downstream = 200,
  arrow_length = 5,
  arrow_unit = "pt",
  gene_color = "#0088ff",
  promoter_color = "#ff8800",
  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
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK