Code to create the images needed to compose the hicExplorer spiral tracks (http://hicexplorer.readthedocs.io/en/latest/_images/hicex2.png). Once the plots are generated they need to be put together using GIMP, Photoshop, or similar program. To run, HiCExplorer and ImageMagick need to be installed

make_hicexplore_spiral_plots.py

import sys
import os
import hicexplorer.trackPlot

dpi = 350
#dpi = 50
increment = int(1.0e6)
start = int(3e6)
frac_decrease = 0.15  # fraction of decrease per image

trp = hicexplorer.trackPlot.PlotTracks("tracks.ini", 80, dpi=dpi)
#trp = hicexplorer.trackPlot.PlotTracks("test/tracks.ini", 80, dpi=dpi)

hicexplorer.trackPlot.DEFAULT_WIDTH_RATIOS = (1, 0.00)
hicexplorer.trackPlot.DEFAULT_MARGINS = {'left': 0, 'right': 1, 'bottom': 0, 'top': 1}

angle = 45
count = 0
width_list = []
height_list = []
image_name_list = []

for start in range(3000000, int(7e6), increment):
    end = start + increment
    chrom='chr2R'
    file_name = "/tmp/{}.png".format(count + 1)
    file_name_convert = "images/{}.png".format(count + 1)
    width, height = trp.plot(file_name, chrom, start, end, title='')
    # transform inches to pixels
    width = int(width * dpi)
    height = int(height * dpi)
    image_name_list.append(file_name_convert)
    resize_width = width * (1 - frac_decrease)**count
    width_list.append(resize_width)
    height_list.append(resize_width)
    count += 1

    perspective = "Perspective '0,0,0,0 0,{0},0,{0} {1},0,{1},{2} {1},{0},{1},{0}'".format(height, width, height * frac_decrease)
    # -transparent white
    convert = "convert {} -distort {}  -resize {}x  -matte -virtual-pixel transparent  miff:- | " \
              "convert - -matte -virtual-pixel transparent -distort Arc '90 {}' {}".format(file_name, perspective,
                                                                                    resize_width,
                                                                                    angle, file_name_convert)
    print convert
    os.system(convert)

    angle += 90



###
#
# the following code to make an spiral automatically does not work
# because the images are not properly placed. Some more work is needed


# the size of the final spiral is:
#  x = width of the 3th image + the width of the 1st image
#  y = height of first image + height of second image
"""
import commands
for img in image_name_list:
    # get size of image
    #import ipdb;ipdb.set_trace()
    res = commands.getstatusoutput('identify -format "%w %h" {}'.format(img))
    width, height = res[1].split()
    width_list.append(int(width))
    height_list.append(int(height))

size = "{x}x{y}".format(x=width_list[2] + width_list[0], y=height_list[0] + height_list[1])
convert_cmd = "convert -size {size} xc:none ".format(size=size)
origin = [width_list[2], 0]
for idx in range(len(width_list)):
    # y for upper right is 0
    # x for upper right is width_list[2]

    convert_cmd += "{image} -geometry +{x}+{y} -composite ".format(image=image_name_list[idx],
                                                                    x=origin[0],
                                                                    y=origin[1])

    if idx == len(width_list) - 1:
        break
    if idx % 4 == 0:
        origin[0] += 2 * (width_list[idx] - width_list[idx + 1]) / 3
        origin[1] += width_list[idx]

    if idx % 4 == 1:
        origin[0] -= width_list[idx + 1]
        origin[1] -= (height_list[idx] - height_list[idx + 1]) / 2

    if idx % 4 == 2:
        origin[0] += (width_list[idx] - width_list[idx + 1]) / 2
        origin[1] -= width_list[idx + 1]

    if idx %4 == 3:
        origin[0] += width_list[idx + 1]
        origin[1] += (height_list[idx] - height_list[idx + 1]) / 2

os.system(convert_cmd + " test/composite.png")
"""

Is there any example inputs?

Thank you so much.