Ectopic 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_fontsize: 8

trackc cli ectopic_interactions.yaml -s 5,1

image-10.png