3D基因组工具（HiC可视化）trackc--bioinfomatics tools 35

01 3D genome data analysis guides

https://trackc.readthedocs.io/en/latest/install.html    #官网
https://github.com/seqyuan/trackc           #官网

https://trackc.readthedocs.io/en/latest/analysis_guide/index.html   #HiC可视化案例

GridSpec

在基因组区域中可视化多组学数据通常需要结合多个轨迹（tracks）。为了创建适合发表的高质量图像，精细调整每个轨迹的比例非常重要。快速调整轨迹比例以及轻松添加或移除轨迹的能力是一个重要问题。

trackc 提供了两种方法来绘制布局：

trackc.tenon
trackc.make_spec

这些函数为用户提供了一种快速灵活的方法，用于调整每个轨迹的比例，同时方便地在多组学可视化布局中添加或移除轨迹。

1. `trackc.tenon`

trackc.tenon 返回一个对象。例如：
复制代码
```
ten = trackc.tenon(width=5, height=1)
```
在此示例中，ten 是一个表示虚拟图形的对象，其宽度为 5，高度为 1。用户可以通过以下方法向该图形添加轨迹：
复制代码
```
ten.add(pos='bottom', height=4, hspace=0.1)
```
- height 参数 表示新添加轨迹的相对高度。例如，如果虚拟图形的高度为 1，而新轨迹的高度为 4，则子图的实际高度将为 1 * 4。
- 使用 ten.add 方法 类似于搭建积木，用户可以通过 pos 参数 选择将新轨迹添加到顶部（top）或底部（bottom）。
- hspace=0.1 参数 控制新轨迹与相邻轨迹之间的间距。

2. `trackc.make_spec`

trackc.make_spec 定义整个图像的大小，允许用户从上到下或从左到右设置一组子图，可以通过 height_ratios 或 width_ratios 控制各部分的比例。

可用轨迹

本节包括多个快速教程，展示了使用 trackc 进行组学数据可视化的功能。

02 安装

trackc 运行需要 Python 版本 >= 3.8。

通过 PyPI 安装

使用以下命令安装 trackc：

pip install trackc
更新 trackc 的命令：

pip install --upgrade trackc
指定版本和安装源的命令：

pip install -i https://pypi.org/simple trackc==版本号

开发版本

从 GitHub 安装 trackc 的命令：

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

03 heatmap

复制代码

conf-hicmap_1.yml等很多

trackc:
  - ax: t1
    height: 2
    track_type: hicmap
    track_para:
      mat:
        method: extractContactRegions
        clr: /path/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000
        row_regions:
          - chr6
          - chr8
      mapC:
        cmap: plasma

复制代码

运行

trackc cli conf-hicmap_1.yml -s 4,1 -o chr6_chr8.pdf

conf-hicmap_4.yml

trackc:
  - ax: t1
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: ./github/seqyuan/trackc_data/examples/HPDE6C7.chr18.mcool::/resolutions/25000
      mapC:
        map_type: tri
        height: 50
        label: tri
  - ax: t2
    height: 1
    hspace: 0.3
    track_type: hicmap
    track_para:
      mat2:
        method: extractCisContact
        clr: ./github/seqyuan/trackc_data/examples/HPDE6C7.chr18.mcool::/resolutions/25000
      mapC:
        map_type: tri
        height: 50
        label: tri-mat2
  - ax: t3
    height: 2
    hspace: 0.3
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: ./github/seqyuan/trackc_data/examples/HPDE6C7.chr18.mcool::/resolutions/25000
      mapC:
        map_type: tri
        height: 50
        label: tri-symmetric
        symmetric: True

  - ax: t4
    height: 1
    hspace: 0.3
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr:./github/seqyuan/trackc_data/examples/BxPC3.chr18.mcool::/resolutions/25000
        extend: 50
      mapC:
        cmap: PuBu
        map_type: rec
        height: 50
        label: rec
  - ax: t5
    height: 1
    hspace: 0.3
    track_type: hicmap
    track_para:
      mat2:
        method: extractCisContact
        clr: ./github/seqyuan/trackc_data/examples/BxPC3.chr18.mcool::/resolutions/25000
        extend: 50
      mapC:
        cmap: cividis
        map_type: rec
        height: 50
        label: rec-mat2
  - ax: t6
    height: 2
    hspace: 0.3
    track_type: hicmap
    track_para:
      mat2:
        method: extractCisContact
        clr: ./github/seqyuan/trackc_data/examples/BxPC3.chr18.mcool::/resolutions/25000
        extend: 50
      mapC:
        cmap: magma
        map_type: rec
        height: 50
        symmetric: True
        logdata: True
        label: rec-symmetric

  - ax: t1
    track_type: scale_track
    track_para:
      scale_adjust: Mb
      tick_pos: top
      ratio2ax: 1

运行

trackc cli conf-hicmap_4.yml -r 18:10000000-14500000

04 rearranged_interactions

ectopic_interactions.yaml

trackc:
  - ax: t1
    height: 2
    track_type: hicmap
    track_para:
      mat:
        method: extractContactRegions
        clr: ./github/seqyuan/trackc_data/examples/BxPC3.chr18.mcool::/resolutions/50000
        balance: False
        row_regions: 18:45000000-78077248
      mapC:
        map_type: tri
        label: tumor res=50k
        cmap: PuBu
        maxrange: 70
        ax_on: False
  - ax: t1
    track_type: scale_track
    track_para:
      region: 18:45000000-78077248
      scale_adjust: Mb
      tick_pos: top
      ratio2ax: 0.3
      space: 0.01
      tick_fontsize: 6
      label_fontsize: 7
  - ax: t2
    height: 0.2
    track_type: zoomin
    track_para:
      raw_regions: 18:45000000-78077248
      zoomin_regions:
        - 18:47340000-50370000
        - 18:61140000-63630000
        - 18:74030000-77560000
      line_on: False
      fill: True
      alpha: 0.5

  - ax: t3
    height: 0.4
    track_type: multi_scale_track
    track_para:
      regions:
        - 18:47340000-50370000
        - 18:61140000-63630000
        - 18:74030000-77560000
      scale_adjust: Mb
      intervals: 2
      tick_fontsize: 7

  - ax: t4
    height: 2
    track_type: hicmap
    track_para:
      mat2:
        method: extractContactRegions
        clr: ./github/seqyuan/trackc_data/examples/BxPC3.chr18.mcool::/resolutions/25000
        balance: False
        row_regions:
          - 18:47340000-50370000
          - 18:61140000-63630000
          - 18:74030000-77560000
      mapC:
        map_type: tri
        label: ectopic interactions
        cmap: PuBu
        ax_on: False
        maxrange: 100

  - ax: t5
    height: 0.2
    track_type: zoomin
    track_para:
      raw_regions:
        - 18:47340000-50370000
        - 18:61140000-63630000
        - 18:74030000-77560000
      zoomin_regions:
        - 18:47400000-48280000
        - 18:75280000-74030000
      line_on: False
      fill: True
      alpha: 0.5

  - ax: t6
    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: t7
    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: t8
    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: t9
    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_fontszie: 8

运行

trackc cli ectopic_interactions.yaml -s 5,1

05 Virtual 4C

4C.yaml

trackc:
  - ax: t1
    height: 4
    track_type: hicmap
    track_para:
      mat:
        method: extractContactRegions
        clr: ./github/seqyuan/trackc_data/tutorials/4C/GSM4604287_1360.sub.cool
        balance: False
      mapC:
        map_type: tri
        label: AML 1360
        cmap: PuBu
        maxrange: 6
        minrange: -6

  - ax: t2
    height: 0.7
    track_type: gene_track
    track_para:
      bed12: ./github/seqyuan/trackc_data/tutorials/4C/GRCh38.gene.chr8chr14.bed12
      line: 3
      gene_fontszie: 10
      show_label:
        - MYC
  - ax: t3
    height: 0.7
    track_type: bw_track
    track_para:
      bw: ./github/seqyuan/trackc_data/tutorials/4C/GSM4604189_H3K27ac.bw
      maxrange: 10
      label: H3K27ac
      binsize: 10000
      invert_y: False
  - ax: t4
    height: 0.6
    track_type: virtual4C
    track_para:
      clr: ./github/seqyuan/trackc_data/tutorials/4C/GSM4604287_1360.sub.cool
      maxrange: 10
      label: Virtual 4C
      target_color: tab:red
      track_type: line
      target: chr8:127735434-127735435

  - ax: t5
    height: 0.6
    track_type: multi_scale_track
    track_para:
      scale_adjust: Mb
      intervals: 1
      tick_fontsize: 8

运行

trackc cli 4C.yaml -s 6,0.75 -r 'chr8:127000000-129200000 chr14:96500000-99300000'

06 常用命令行

import trackc as tc

ten = tc.tenon(figsize=(8,1))
ten.add(pos='bottom', height=3.6)
ten.add(pos='bottom', height=1)

chr6_len = clr.chromsizes['chr6']
chr8_len = clr.chromsizes['chr8']

mat = tc.tl.extractContactRegions(clr='GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000', row_regions=['chr6', 'chr8'])
tc.pl.mapC(ax=ten.axs(0), mat=mat.cmat, map_type='triangle', maxrange=5000)

tc.pl.multi_scale_track(ax=ten.axs(1), regions=['chr6:0-{0}'.format(chr6_len), 'chr8:0-{0}'.format(chr8_len)],
                        scale_adjust='Mb', intervals=2, tick_rotation=0)
# tc.savefig('hicmap.pdf')