trackc 0.0.25

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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