plot_genome: genome model plotter

In RubD/GeTrackViz2:

Description

This function plots the genomic model

Usage

plot_genome(transcript, exon, five_UTR, three_UTR, mychr = "chr14",
  start_loc = 61100000, end_loc = 61195000, breaks_wanted = 4,
  show_partial_overlap = T, marginvec_mm = c(0, 0, 0, 0),
  y_coord_gene_dist = 0.5, y_top_space = 2, y_genename_space = 1,
  genename_size = 4, exon_size = 0.5, UTR_size = 0.5,
  reverse_strand = FALSE, show_labels = T, print_plot = T)

Arguments

transcript	transcript in bed format
exon	exon coordinates in bed format
five_UTR	five_UTR coordinates in bed format
three_UTR	three_UTR coordinates in bed format
mychr	chromosome
start_loc	start location on chromomse
end_loc	end location on chromosome
breaks_wanted	number of breaks on x-axis
show_partial_overlap	include loops that do not entirely overlap the coordinates
marginvec_mm	margin around plot, default = c(0,0,0,0)
y_coord_gene_dist	distance between genes
y_top_space	additional space on top
y_genename_space	space between gene name and gene model
genename_size	size of gene name
show_labels	boolean: show x-axis lables
print_plot	boolean: print individual plot

Value

ggplot object

Examples

    plot_genome(mychr, ...)

RubD/GeTrackViz2 documentation built on May 31, 2019, 2:45 p.m.