links
Description
A track for pairs of intervalls, the supported format is (tab separated): chr1 start1 end1 chr2 start2 end2 (score …) The score field is optional and fields after the score are ignored.
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.
links_type: arcs (default) or triangles, loops or squares.
line_width: by default this option is not set but you can also put: any float above 0
line_style: solid (default) or dashed, dotted or dashdot.
color: blue (default)
alpha: 0.8 (default) or any float above 0 below 1
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
ylim: by default this option is not set but you can also put: any float above 0
compact_arcs_level: 0 (default) or 1 or 2.
use_middle: false (default) or true.
region2: by default this option is not set
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
# the file format for links is (tab separated)
# chr1 start1 end1 chr2 start2 end2 (score ...)
# The score field is optional
# The fields after the score field will be ignored
# for example:
# chr1 100 200 chr1 250 300 0.5
# depending on the value of links_type either 'arcs' or 'triangles' or 'loops'
# or 'squares' can be plotted.
# If arcs, an arc will be drawn linking the beginning of the first region (chr1: 100),
# to the end of the other region (chr1: 300) except if use_middle is set to true.
# If triangles, the vertix of the triangle will be drawn at the center between the two points
# (also the extremity of each position is used)
# If loops, a diamond highlighting the intersection between the 2 regions will be shown
# the triangles, and loops options are convenient to overlay over a
# Hi-C matrix to highlight the matrix pixel of the highlighted link.
# If squares, a rectangle highlighting the intersection between the 2 regions will be shown
# In this case the y axis represent region2 which can be specified
# By default it is the same as the region of the x-axis
#region2 = X:3000000-3500000
# For these tracks do not hesitate to put large line_width like 5 or 10.
links_type = arcs
# For triangles and arcs, by default the extremities coordinates are used
# To use the middle of start1 and end1 and the middle of start2 and end2
#use_middle = true
# color of the lines
color = red
# if color is a valid colormap name (like RdYlGn),
# then the score is mapped to the colormap.
#color = RdYlGn
# To set the minimum and maximum value of the colormap:
#min_value = 0
#max_value = 1.2
# To use transparency, you can use alpha
# default is 0.8
# alpha = 0.5
# if line_width is not given, the score is used to set the line width
# using the following formula (0.5 * square root(score)
#line_width = 0.5
# options for line_style are 'solid', 'dashed', 'dotted', and 'dashdot'
line_style = solid
# If you want to compact the arcs (when you have both long and short arcs)
# You can choose a compact level of
# 1 (the height is proportional to the square root of the distance)
# 2 (the height is the same for all distances)
# (default is 0 proportional to distance)
#compact_arcs_level = 2
# To be able to see small arcs when big arcs exists, you can set
# the upper y limit.
# The unit is bp. This corresponds to the longest arc you will see.
# This option is incompatible with compact_arcs_level = 2
#ylim = 100000
file_type = links