参考资料：

• https://docs-python.higlass.io/
• https://docs-python.higlass.io/getting_started.html#simplest-use-case

软件安装

conda create -n higlass python=3.8

pip install jupyter higlass-python

jupyter nbextension install --py --sys-prefix --symlink higlass
jupyter nbextension enable --py --sys-prefix higlass

启动 jupyter notebook

jupyter notebook

Examples

chromosome-annotate + gene-annotate + bar-plot + bed-region + 2d-heatmap

截屏2021-08-10 下午6.44.43.png

45-rotated-heatmap + bed-region + line-plot

截屏2021-08-10 下午6.43.59.png

Tracks

import higlass
from higlass.client import View, Track
from higlass.tilesets import cooler, chromsizes, beddb, bigwig, bigbed

track:chromsome-annotate

(mm10)

track_chrom = Track(
    position = 'top',
    track_type = 'horizontal-chromosome-labels',
    tilesetUid = "EMo5uFThS5S263tNLbzeVw",
    server = "https://higlass.4dnucleome.org/api/v1",
)

### track: gene-annotate
```python
track_gene = Track(
    position = 'top',
    track_type = "horizontal-gene-annotations",
    tilesetUid='OHJakQICQD6gTD7skx4EWA',
    server='https://higlass.io/api/v1',
    height=100,
    
)

track: 2d-heatmap

hic = cooler('4DNFITHTURR9.mcool')
track_hic = Track(
    position = 'center',
    track_type = 'heatmap',
    tileset = hic
)

45-rotated-heatmap

hic = cooler('output/agg_contact_matrix/Nagano_129G1_chr19.1000.mcool')
track_hic = Track(
    position = 'top',
    track_type = "horizontal-heatmap",
    tileset = hic,
    height=200,
    options = {
        'name': 'Pool of 129 G1 cells',
         "labelPosition": "topLeft", 
    }
)

2d-domain (TAD)

数据预处理： BED → BEDPE-like file

clodius aggregate bedpe \
  --chromsizes-filename galGal6.chrom.sizes \
  --chr1-col 1 --chr2-col 1 \
  --from1-col 2 --to1-col 3 \
  --from2-col 2 --to2-col 3 \
  domain.bed

得到 domain.bedpe.beddb

domain = beddb('domain.bedpe.beddb')
track_domain = Track(
    position = 'top',
    track_type = 'bedlike',
    tileset = domain,
    height=50
)

bed region

数据预处理：BED → BED-like file

clodius aggregate bedfile \
    --chromsizes-filename ${chrsize_file} \
    boundary.bed

得到 boundary.bed.beddb

domain_boundary = beddb('boundary.bed.beddb')
track_domain_boundary = Track(
    position = 'top',
    track_type = 'bedlike',
    tileset = domain_boundary,
    height=40,
    options = {
        "name": 'TopDom domain boundary', 
        "labelPosition": "topLeft", 
        "fillColor": "red"
    }
)

line plot

数据预处理：BEDGRPAH → BIGWIG

in_bedgraph=boundary_freq.bedgraph
out_bigwig=boundary_freq.bigwig
bedGraphToBigWig ${in_bedgraph} ${chrsize_file} ${out_bigwig}

得到 boundary_freq.bigwig

f = open('/Users/ziyin/Documents/Lab/project/scHiC/data/reference/mm10.chrom.sizes')
chromsizes = []
for line in f.readlines():
    row = line.strip().split('\t')
    chromsizes.append( (row[0], int(row[1]) ) )

ts = bigwig(boundary_freq.bigwig, chromsizes=chromsizes)
track =  Track(
        position = 'top',
        track_type = 'line',
        tileset = ts,
        height=80,
        options = {
            "name": mode, 
            "labelPosition": "topLeft", 
            "lineStrokeColor": 'red',
            "trackBorderWidth": 1,
            "trackBorderColor": "gray",
        }
    )

bar-plot

comaprtment = bigwig('4DNFI9685Y2G.bw')
track_compartment = Track(
    position = 'top',
    track_type = 'divergent-bar',
    tileset = comaprtment,
    height = 50,
)

Plot

view = View(
    [
        track_hic,
        track_domain,
        track_chrom,
        track_gene_annotation,
    ],
    chrominfo = track_chrom,
    initialXDomain = [0, 10000000], 
    initialYDomain = [0, 10000000], 
)
display, server, viewconf = higlass.display([view])
display