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Plot chromosome structures and gene annotation

Source: R/plot_chrom_genes.R
plot_chrom_genes.Rd

Plot chromosome structures and gene annotation.

Usage

plot_chrom_genes(
  gff_file,
  gene_table,
  format = "auto",
  annotate = "id",
  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,
  connector_dx1 = 0.2,
  connector_dx2 = 0.2,
  min_gap_frac = 0.02
)

Arguments

gff_file

Genomic structural annotation GFF3/GTF file path.

gene_table

A data.frame: first column gene ID, second column gene name.

format

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

annotate

Which to annotate on the right: ("id", "name").

orientation

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

bar_width

Chromosome bars relative width. (0.6).

chrom_alpha

Chromosome bars alpha. (0.1).

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).

connector_dx1

First connector horizontal offset. (0.15).

connector_dx2

Second connector horizontal offset. (0.15).

min_gap_frac

Minimum vertical gap between labels (fraction of chromosome length). (0.02).

Value

A ggplot object of chromosomes with gene labels.

Examples

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

genes <- data.frame(
  gene_id = c("ENSMUSG00000042414", "ENSMUSG00000025935", "ENSMUSG00000048701", "ENSMUSG00000035385"),
  gene_name = c("Prdm14", "Tram1", "Ccdc6", "Ccl2"))

# Vertical, annotate by name
plot_chrom_genes(
  gff_file = gff_file,
  gene_table = genes,
  annotate = "name",
  orientation = "vertical")
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK


# Horizontal, annotate by id
plot_chrom_genes(
  gff_file = gff_file,
  gene_table = genes,
  annotate = "id",
  orientation = "horizontal")
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK
#> Coordinate system already present.
#> ℹ Adding new coordinate system, which will replace the existing one.