bedgraph_matrix

Description

A track for file like bedgraph but with more than 4 columns, like the insulation score from hicPlotTADs

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.

  • 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

  • show_data_range: true (default) or false.

  • type: matrix (default) or lines.

  • rasterize: true (default) or false.

  • pos_score_in_bin: center (default) or block.

  • plot_horizontal_lines: false (default) or true.

  • colormap: viridis (default)

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

# a bedgraph matrix file is like a bedgraph, except that per bin there
# are more than one value separated by tab: E.g.
# This file type is produced by HiCExplorer tool hicFindTads and contains
# the TAD-separation score at different window sizes
# chrX	18279	40131	0.399113	0.364118	0.320857	0.274307
# chrX	40132	54262	0.479340	0.425471	0.366541	0.324736
#min_value = 0.10
#max_value = 0.70
# if type is set as lines, then the TAD score lines are drawn instead
# of the matrix otherwise a heatmap is plotted
type = lines
# If the type is not lines, you can choose to keep the matrix as not rasterized
# (only used if you use pdf or svg output format) by using:
# rasterize = false
# The different options for color maps can be found here:
# https://matplotlib.org/users/colormaps.html
# the default color map is viridis
# If you want your own colormap you can put the values of the color you want
# For example, colormap = ['blue', 'yellow', 'red']
# or colormap = ['white', (1, 0.88, 2./3), (1, 0.74, 0.25), (1, 0.5, 0), (1, 0.19, 0), (0.74, 0, 0), (0.35, 0, 0)]
#colormap = Reds
# pos_score_in_bin means 'position of score with respect to bin start and end'
# if the lines option is used, the y values can be put at the
# center of the bin (default) or they can be plot as 'block',
# which mean to plot the values as a line between the start and end of bin
pos_score_in_bin = center
show_data_range = true

# only when type lines is used. Adds horizontal lines
plot_horizontal_lines = false
file_type = bedgraph_matrix