hic_matrix

Description

A track for matrix files. Only cool format and h5 format from HiCExplorer are supported. For other format, please first convert to a supported format, for example with hicConvertFormat <https://hicexplorer.readthedocs.io/en/latest/content/tools/hicConvertFormat.html#hicconvertformat>.

Parameters

Necessary:

  • file

Optional:

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

  • height: If you do not set it, the height will be adjusted so that each bin is a square, else you can choose any 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

  • transform: no (default) or log, log1p or -log.

  • rasterize: true (default) or false.

  • colormap: RdYlBu_r (default)

  • depth: 100000 (default) or any integer above 1

  • show_masked_bins: false (default) or true.

  • scale_factor: 1 (default) or any float

Output of make_tracks_file:

# The different options for color maps can be found here:
# https://matplotlib.org/users/colormaps.html
# the default color map is RdYlBu_r (_r) stands for reverse
# 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 = RdYlBu_r
# depth is the maximum distance that should be plotted.
# If it is more than 125% of the plotted region, it will
# be adjsted to this maximum value.
depth = 100000
# height of track (in cm) can be given.
# Otherwise, the height is computed such that the proportions of the
# hic matrix are kept (e.g. the image does not appear shrink or extended)
# height = 10
# min_value and max_value refer to the contacts in the matrix.
#min_value =2.8
#max_value = 3.0
# the matrix can be transformed using the log1p (or log or -log, but zeros could be problematic)
transform = log1p
# show masked bins plots as white lines
# those bins that were not used during the correction
# the default is to extend neighboring bins to
# obtain an aesthetically pleasant output
show_masked_bins = false
# optional if the values in the matrix need to be scaled the
# following parameter can be used. This is useful to plot multiple hic-matrices on the same scale
# scale_factor = 1
# You can choose to keep the matrix as not rasterized
# (only used if you use pdf or svg output format) by using:
# rasterize = false
file_type = hic_matrix