track_links {rGenomeTracks}R Documentation

Generate links track

Description

Generate links track from arc file.

Usage

track_links(
  file,
  title = NULL,
  height = 2,
  overlay_previous = "no",
  orientation = NULL,
  links_type = "arcs",
  line_width = NULL,
  line_style = "solid",
  color = "blue",
  alpha = 0.8,
  max_value = NULL,
  min_value = NULL,
  ylim = NULL,
  show_data_range = FALSE,
  compact_arcs_level = 0,
  use_middle = FALSE
)

Arguments

file

String. The location of the track file

title

String. If specificed, the title of the track to be displayed.

height

Numeric. The height of the plotted track in cm. Default is 2. See notes.

overlay_previous

String. Options are "no" (default) or "yes" or "share-y".

orientation

String. Default is NULL. Other option is "inverted".

links_type

String value with options "arcs" (default) or "triangles" or "loops".

line_width

Numeric value for line width.

line_style

String with options of either "solid", "dashed", "dotted", and "dashdot".

color

String. Hex color or string color. Default is "#1f78b4".

alpha

Numeric variable between 0 and 1 to indicate level of transparancy. Default is 1.

max_value

Numeric. Default is NULL. The max value cut-off for the numeric column.

min_value

Numeric. Default is NULL. The max value cut-off for the numeric column.

ylim

Numeric value above 0 to set arcs' height cutoff. Default is NULL

show_data_range

Boolean. Default is TRUE.

compact_arcs_level

Numeric value of either 0, 1 or 2 to indicate level of arcs' compactness by distance it travels.

use_middle

Boolean. Default is FALSE.

Details

Level of compactness relative to arcs' length can be manipulated using the argument compact_arcs_level where:

ylim argument sets the cutoff for arcs' height. This could be handy if you have small arc overridden by larger arc.

Value

genome_track

Note

ylim argument is incompatible with compact_arcs_level = 2

Author(s)

Omar Elashkar

Examples

tads_dir <- system.file("extdata", "tad_classification.bed",
  package = "rGenomeTracks"
)
genes_dir <- system.file("extdata", "dm3_genes.bed.gz",
  package = "rGenomeTracks"
)
links_dir <- system.file("extdata", "test.arcs",
  package = "rGenomeTracks"
)
tads <- track_domains(tads_dir, color = "#cccccc", border_color = "red")
links_overlay <- track_links(links_dir,
  color = "red",
  line_width = 3, links_type = "loop",
  overlay_previous = "share-y"
)
links <- track_links(links_dir,
  color = "blue",
  line_width = 3, height = 3
)
genes <- track_bed(genes_dir,
  height = 7, style = "flybase",
  fontsize = 10
)
vlines <- track_vlines(genes_dir)
## Not run: 
plot_gtracks(tads + links_overlay + links + genes + vlines, chr = "X", start = 30 * 10^5, end = 35 * 10^5)

## End(Not run)

[Package rGenomeTracks version 1.0.0 Index]