narrow_peak

Description

A track for ENCODE narrowPeak format.

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: 1 (default) or any float above 0

  • color: #FF000080 (default)

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

  • show_data_range: true (default) or false.

  • show_labels: true (default) or false.

  • use_summit: true (default) or false.

  • width_adjust: 1.5 (default) or any float above 0

  • type: peak (default) or box.

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

color = #FF000080
#max_value = 0.70
show_data_range = true
show_labels = true
# the narrowPeak format provides the information of the
# peak summit. By default this information is used
# although some peaks may look crooked.
use_summit = true
# type of plot: either box or peak
# box will plot a rectangle of the peak width
# peak will plot the shape of the peak, whose height is the
# narrowPeak file signal value (usually peak coverage)
type = peak
# if the peaks look too thin, the can be adjusted
width_adjust = 1.5
# optional: line_width
#line_width = 0.5
file_type = narrow_peak