domains

Description

A track for bed files that you want to see as triangles.

Parameters

Necessary:

  • file

Optional:

  • title: Put here a title which will apprear on the right.

  • height: 0.5 (default) or float above 0.

  • overlay_previous: no (default) or yes or share-y.

  • orientation: by default this option is not set but you can also put: inverted.

  • line_width: 0.5 (default) or any float above 0

  • color: #1f78b4 (default)

  • max_value: by default this option is not set but you can also put: any float

  • min_value: by default this option is not set but you can also put: any float

  • border_color: black (default)

  • prefered_name: transcript_name (default)

  • merge_transcripts: false (default) or true.

Output of make_tracks_file:

# title of track (plotted on the right side)
title =
# height of track in cm (ignored if the track is overlay on top the previous track)
height = 2
# if you want to plot the track upside-down:
# orientation = inverted
# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
# Otherwise, each plot use its own scale
#overlay_previous = yes

# If the bed file contains a column for color (column 9), then this color can be used by
# setting:
#color = bed_rgb
# if color is a valid colormap name (like RbBlGn), then the score (column 5) is mapped
# to the colormap.
# In this case, the the min_value and max_value for the score can be provided, otherwise
# the maximum score and minimum score found are used.
#color = RdYlBu
#min_value=0
#max_value=100
# If the color is simply a color name, then this color is used and the score is not considered.
color = darkblue
# optional: line_width
#line_width = 0.5
# optional, default is black. To remove the border, simply set 'border_color' to none
#border_color = black
# optional. If not given it is guessed from the file ending.
file_type = domains