track_domains {rGenomeTracks}R Documentation

Generate domains track

Description

Domain files are bed files represents TADS in the case of HiC analysis.

Usage

track_domains(
  file,
  title = NULL,
  height = 2,
  overlay_previous = "no",
  orientation = NULL,
  line_width = 0.5,
  color = "#1f78b4",
  max_value = NULL,
  show_data_range = TRUE,
  min_value = NULL,
  border_color = "black",
  prefered_name = "transcript_name",
  merge_transcripts = 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. Set to "inverted" to make the track upside down. Default is NULL.

line_width

Numeric. Default is 0.5.

color

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

max_value

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

show_data_range

Boolean. Default is TRUE.

min_value

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

border_color

String. default is "black"

prefered_name

String. Denote which column to get elements names. Default is "transcript_name".

merge_transcripts

Boolean. Default is FALSE.

Details

To remove the border, set 'border_color' parameter to "none".

Value

genome_track

Author(s)

Omar Elashkar

Examples

tads_dir <- system.file("extdata", "tad_classification.bed",
  package = "rGenomeTracks"
)
tads <- track_domains(
  file = tads_dir, border_color = "black",
  color = "#11FF34", height = 5
)
tads_i <- track_domains(
  file = tads_dir, border_color = "red",
  color = "#cccccc", height = 3, orientation = "inverted"
)
tracks <- track_x_axis(where = "top") +
  tads + tads_i
## Not run: 
plot_gtracks(tracks, chr = "X", start = 30 * 10^5, end = 35 * 10^5)

## End(Not run)

[Package rGenomeTracks version 1.0.0 Index]