trackc

Track view of chromosome conformation and multi-omics data

trackc is a python package for flexible visualization of rearrangement 3D genome and multi-omics data. It builds on top of matplotlib, which allows for flexible adjustments.

trackc’s key applications

Mark the abnormal interaction formed by the structural variation of the genome.
Show the 3Dgenome interaction and multi-omics data after rearrangement.
Flexible and convenient layout for multi-track

Available track types

tracks
track	functions	Description
Hi-C heatmap	tl.extractContactRegions, tl.extractCisContact, mapC	support multi-regions and reverse regions
mark regions on heatmap	mapc_markline	support multi-regions and reverse regions, mark square line on mapc heatmap
Virtual4C	Virtual4C	support multi-regions and reverse regions
loop links	links_track	support multi-regions and reverse regions
bed	bed_track	support multi-regions and reverse regions, styles[bar, line, rectangle, triangle, link] to show ChIP-seq peak or ATAC-seq peaks, TAD domains, SVs bed or begGraph
bigwig	bigwig_track	support multi-regions and reverse regions
bedgraph matrix	bdgmat_track	support multi-regions and reverse regions, styles [heatmap, line]
zoomin visualization	zoomin	support multi-regions and reverse regions
gene annotation	gene_track	support multi-regions and reverse regions
scale bar	scale_track	genome position scale
multi scale bar	multi_scale_track	support multi-regions and reverse regions
high light some position or regions	vhighlight	support multi-regions and reverse regions

Here is an example of du_dynamic_2022 article diagram implemented by trackc.

Installation

PyPI

Install trackc by running:

pip install trackc

Development version

To install trackc from GitHub, run:

pip install git+https://github.com/seqyuan/trackc@main

Usage

trackc support both api and cli. Here is a cli example:

trackc cli conf.yml

conf.yml content

trackc:
  - ax: l1
    height: 1.25
    track_type: hicmap
    track_para:
      mat:
        method: extractContactRegions
        clr: ./github/seqyuan/trackc_data/examples/BxPC3.chr18.mcool::/resolutions/25000
        balance: False
        row_regions:
          - 18:47400000-48280000
          - 18:75280000-74030000
      mapC:
        map_type: tri
        label: neo tad
        cmap: PuBu
        height: 40
        ax_on: False
        maxrange: 200
        minrange: 10

  - ax: l2
    height: 0.5
    track_type: bw_track
    track_para:
      bw: ./github/seqyuan/trackc_data/examples/GSM3178671_BxPC3_H3K27ac.bigwig
      regions:
        - 18:47400000-48280000
        - 18:75280000-74030000
      label: H3K27ac
      binsize: 2000
      color:
        - '#5B7695'
  - ax: l3
    height: 0.4
    track_type: multi_scale_track
    track_para:
      regions:
        - 18:47400000-48280000
        - 18:75280000-74030000
      scale_adjust: Mb
      intervals: 2
      tick_fontsize: 7

  - ax: l4
    height: 2.8
    track_type: gene_track
    track_para:
      bed12: ./github/seqyuan/trackc_data/examples/hg19_chr18.gene.bed12
      regions:
        - 18:47400000-48280000
        - 18:75280000-74030000
      line: 12
      gene_fontsize: 8

Documentation

Our documentation provide the full list of possible track types and gallary guidelines for users.

Extensive documentations are available at https://trackc.readthedocs.io

Citation

If you use trackc in your analysis, Please cite trackc as follows:

trackc: a package for flexible visualization of rearrangement 3D genome and multi-omics data

Metadata

Release files for trackc 0.0.28

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Source distribution for trackc 0.0.28
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Table of built distributions (wheels) for trackc 0.0.28
File	Interpreter	ABI	Platform	Reset
trackc-0.0.28-py3-none-any.whl 55.4 kB Jun 6, 2026 With provenance	Python 3	none	any	Details

Total release size: 99.0 kB

Release files / trackc-0.0.28.tar.gz

Download URL	trackc-0.0.28.tar.gz
Size	43.6 kB
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Publishing repository: github.com/seqyuan/trackc
Publishing commit: github.com/seqyuan/trackc/tree/672180881c8929f22cd007271ca604c46bae38bc

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SHA-256 checksum: 89def91154e9aee69b0cf7cd919e79cba17915c8fb93991decbe1d87b9a2a8a2 Verifying attestations

Release files / trackc-0.0.28-py3-none-any.whl

Download URL	trackc-0.0.28-py3-none-any.whl
Size	55.4 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`03c8c1c1ee4a4ff20bc8fb0ed953b4c66d88743c8a12df09ecf5e0bd4348ebdb`
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Upload date	Jun 6, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/seqyuan/trackc
Publishing commit: github.com/seqyuan/trackc/tree/672180881c8929f22cd007271ca604c46bae38bc

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Publishing configuration: github.com/seqyuan/trackc/blob/672180881c8929f22cd007271ca604c46bae38bc/.github/workflows/ci.yml
Publishing logs: github.com/seqyuan/trackc/actions/runs/27057271255/attempts/1

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Report project as malware

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Publishing platform: GitHub Actions
Publishing repository: github.com/seqyuan/trackc
Publishing commit: github.com/seqyuan/trackc/tree/672180881c8929f22cd007271ca604c46bae38bc

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Publishing configuration: github.com/seqyuan/trackc/blob/672180881c8929f22cd007271ca604c46bae38bc/.github/workflows/ci.yml
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