A few bugs in loops (arcs) and Hi-C Heatmap body.

[Linhua-Sun]

Hi @Nanguage

Question 1 and 2

I am trying to use CoolBox to plot loops above the heatmap like JuiceBox (https://github.com/aidenlab/Juicebox/wiki/Loading-Annotations-(Annotations-menu)). While, I found sever bugs.

1. when I use HiCPeaksCoverage to show loops above heatmap body in style of triangular. Only two of all 11 loops are shown, while if we use heatmap body in style of matrix, all loops were shown.
2. Another associated problem came from Arcs function with/without diameter_to_height, as you can seen from the tracks, Loop 1 only shows two loops.

The Loop bedpe file are:

18	2160000	2320000	18	1670000	1790000	*	100
18	2490000	2710000	18	1690000	1770000	*	100
18	2910000	3100000	18	1660000	1770000	*	100
18	3930000	4130000	18	1710000	1790000	*	100
18	3960000	4080000	18	2500000	2680000	*	100
18	3980000	4130000	18	4830000	4940000	*	100
18	4010000	4110000	18	4530000	4680000	*	100
18	4460000	4710000	18	1710000	1810000	*	100
18	4510000	4640000	18	2500000	2660000	*	100
18	4780000	4930000	18	2500000	2680000	*	100
18	4830000	4950000	18	1680000	1830000	*	100

My code is:

## coolbox 0.3.8
# -*- coding: utf-8 -*-

import coolbox
from coolbox.api import *
#from __future__ import print_function
import sys
import re

Ctrl_mcool='test.mcool'
HandLoop='testLoops.bedpe'
BEDfile='testAnchors.bed'

HandLoops1 =  Arcs(HandLoop, open_region=False,color="red",title="conD Loop",score_to_width=1,line_width=1,height=2,orientation="inverted",diameter_to_height="max_height-1")
HandLoops2 =  Arcs(HandLoop, open_region=False,color="red",title="conD Loop",score_to_width=1,line_width=1,height=2,orientation="inverted")
HandArc = HiCPeaksCoverage(HandLoop,color="black",line_width=1,score_to_width=1)
AnchorsBED=BED(BEDfile,display="collapsed",color="blue",border_color='blue',height=0.5,title='Anchors')

cool1 = XAxis() + Cool(Ctrl_mcool,style='triangular',
    balance=True,
    normalize="expect",
    transform=False,
    gaussian_sigma=1,
    norm=False,
    max_value=100,
    resolution=20000,
    cmap='bwr',
    min_value=10,
    color_bar='no')  + HandArc  + Spacer(height=0.1)+ AnchorsBED +HandLoops1  + HandLoops2

cool1.plot('18:1000000-6000000')

The figure is:

[Linhua-Sun]

Question 3

Another question came from loops in upper or lower showing above the heatmap. The key code line is HandArc = HiCPeaksCoverage(HandLoop,color="black",line_width=1,score_to_width=1,side="upper"). I have set side='upper', while the output is still confusing. It is OK if side='both'. It will be quite clean if we can show loops only in one side.

My code is:

## coolbox 0.3.8
# -*- coding: utf-8 -*-

import coolbox
from coolbox.api import *
#from __future__ import print_function
import sys
import re

Ctrl_mcool='test.mcool'
HandLoop='testLoops.bedpe'
BEDfile='testAnchors.bed'

HandLoops =  Arcs(HandLoop, open_region=False,color="red",title="conD Loop",score_to_width=1,line_width=1,height=2,diameter_to_height="max_height-1")

HandArc = HiCPeaksCoverage(HandLoop,color="black",line_width=1,score_to_width=1,side="upper")

AnchorsBED=BED(BEDfile,display="collapsed",color="blue",border_color='blue',height=0.5,title='Anchors')

frame = Arcs(HandLoop, open_region=False,color="red",title="Loop",score_to_width=1,line_width=1,height=2,diameter_to_height="max_height-1") +\
AnchorsBED +\
Spacer() +\
HighLightsFromFile(BEDfile,color='green') 

cool1 = Cool(Ctrl_mcool,style='matrix',
    balance=True,
    normalize="expect",
    transform=False,
    gaussian_sigma=1,
    norm=False,
    max_value=100,
    resolution=20000,
    cmap='bwr',
    min_value=10,
    color_bar='no') + HandArc +  HighLightsFromFile(BEDfile,color='green', alpha=0,border_line_alpha=1,border_line_color='red',border_line_width=1,border_line_style='solid') 

sub_frames = {
    "top": frame,
    "right": frame
}

jv = JointView(cool1,**sub_frames, space=0, padding_left=0)

jv.plot('18:50000000-58000000')

The figure is:

Thanks for your time!
Best wishes!
Linhua