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)

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