Download the official demo input.

Additional demo files are provided in the GitHub project.

Introduction

The "SV: Heatmap" may demonstrate the read and barcode linkage of SV events for WGS pair-end reads and 10x linked reads, respectively. We adopt heatmap to manifest the sequential read/barcode linkages on the surrounding region of the two breakpoints for the given SV event. As indicated in the color bar, the darker the heatmap entry, the more supported ties. Users may upload the specified input file that holding several SV events, then manage the sidebar to customize the heatmap color scheme and select the desired SV event to present.

SV:Heatmap Data (TXT file)

The uploaded TXT file must match the required format. Several demo files from References are provided in the GitHub project.

User can generate the heatmap.txt files using linkage_heatmap.py with BAM file and SvABA generated sv VCF file. Please check https://github.com/paprikachan/ComplexSV for source code and usage of linkage_heatmap.py.

The demo output file demo_data/10x.txt starts with "sv" section.

#sv
chr11   76139879    +   chr2    63328429    -   VARTYPE=BND:TRX-tt

It stores the breakpoints information of SV event, ordered by:

chrom_5p bkpos_5p strand_5p chrom_3p bkpos_3p strand_3p meta_info
chr11 76139879 + chr2 63328429 - VARTYPE=BND:TRX-tt

where chrom_5p, bkpos_5p, strand_5p respectively stands for the chromosome, position, strand of 5' breakpoint, and chrom_3p, bkpos_3p, strand_3p respectively stands for the chromosome, position, strand of 3' breakpoint. meta_info stores the meta information, such as the variation type of the SV.

The second section is "heatmap" section, it starts with the comment:

#heatmap    linkage_type=10x barcode

where linkage_type specifies the type of read linkage used to count, now we support to show "10x barcode" and "Pair End" linkage type.

For a SV event with two breakpoints, expand the breakpoint with 1000bp, we can generate four region pairs and their shared linkage count matrix.

Region pair 1: vertical region is (bkpos_5p-1000bp, bkpos_5p+1000bp) and horizontal region is (bkpos_5p-1000bp, bkpos_5p+1000bp).

v=chr2:63327429-63329429    h=chr2:63327429-63329429    resolution=100  axis=left-top
63.0,34.0,35.0,32.0,21.0,...
34.0,82.0,56.0,37.0,36.0,...
35.0,56.0,104.0,47.0,40.0,...
32.0,37.0,47.0,84.0,40.0,...
21.0,36.0,40.0,40.0,83.0,...
...

Region pair 2: vertical region is (bkpos_5p-1000bp, bkpos_5p+1000bp) and horizontal region is (bkpos_3p-1000bp, bkpos_3p+1000bp).

v=chr2:63327429-63329429    h=chr11:76138879-76140879   resolution=100  axis=right-top
8.0,14.0,7.0,8.0,11.0,...
9.0,17.0,13.0,14.0,13.0,...
14.0,16.0,17.0,22.0,15.0,...
9.0,14.0,11.0,13.0,13.0,...
8.0,13.0,13.0,16.0,13.0,...
...

Region pair 3: vertical region is (bkpos_3p-1000bp, bkpos_3p+1000bp) and horizontal region is (bkpos_5p-1000bp, bkpos_5p+1000bp).

v=chr11:76138879-76140879   h=chr2:63327429-63329429    resolution=100  axis=left-bottom
8.0,9.0,14.0,9.0,8.0,...
14.0,17.0,16.0,14.0,13.0,...
7.0,13.0,17.0,11.0,13.0,...
8.0,14.0,22.0,13.0,16.0,...
11.0,13.0,15.0,13.0,13.0,...
...

Region pair 4: vertical region is (bkpos_3p-1000bp, bkpos_3p+1000bp) and horizontal region is (bkpos_3p-1000bp, bkpos_3p+1000bp).

v=chr11:76138879-76140879   h=chr11:76138879-76140879   resolution=100  axis=right-bottom
80.0,52.0,27.0,42.0,33.0,...
52.0,140.0,56.0,61.0,50.0,...
27.0,56.0,124.0,72.0,50.0,...
42.0,61.0,72.0,152.0,57.0,...
33.0,50.0,50.0,57.0,112.0,...
...

Display Interactions

There are two types of interactions: Tooltips and Download.

  • Tooltips Tooltips will show necessary information of object that the mouse points to.
    • SV Point: Chromosome of 5' breakpoint, position of 5' breakpoint, chromosome of 3' breakpoint, position of 3' breakpoint, and variation type of SV event.
    • Heatmap Window: Window start and end position of 5' and 3' region.
  • Download One SVG file will be generated when the 'Download' button is clicked. Two themes are supplied: the default theme with dark background and the light theme with white backgroud.
  • Light Theme To use the light theme, please click the 'Light Theme' button.

Sidebar Functions

The sidebar provides diverse options to fine-tune the display, such as manage files, reset color, select SV event, show gene annotation and so on.

  • Files
    • Upload: upload heatmap TXT file, and manage uploaded files. Note that duplicated file name will be alerted and given a random postfix.
    • Choose: choose files uploaded previously. Note that this function is ONLY available to registered user (each account has certain storage).
    • File Sets: NOT available to this page.
  • Settings
    • Color for Min Value: reset color of min value.
    • Color for Max Value: reset color of max value.
    • Show gene annottaions: tick to show gene annotations.
  • Genes Show 5' and 3' gene if available, user can select desired gene transcript.
  • SV Points A table of SV events can be selected to visualize. Table headers Gp, 5', Pos, 3', Pos, Type respectively refer to the SV group id, chromosome of 5' breakpoint, position of 5' breakpoint, chromosomeof 3' breakpoint, position of 3' breakpoint, variation type of SV event. "blue" and "yellow" stands for positive and negative strand respectively. Users can click the header to reorder the table.

Manual version=1.0.3, written by Miss. CHEN Lingxi on 2020-02-26.

  1. Zheng, G. X., Lau, B. T., Schnall-Levin, M., Jarosz, M., Bell, J. M., Hindson, C. M., ... & Mudivarti, P. A. (2016). Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nature biotechnology, 34(3), 303. (PMID: 26829319, see Figure 3a)
  2. Spies, N., Weng, Z., Bishara, A., McDaniel, J., Catoe, D., Zook, J. M., ... & Sidow, A. (2017). Genome-wide reconstruction of complex structural variants using read clouds. Nature methods, 14(9), 915. (PMID: 28714986, see Figure 1a-f)
  3. Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., ... & Clark, R. (2018). Integrative detection and analysis of structural variation in cancer genomes. Nature genetics, 50(10), 1388. (PMID: 30202056, see Figure 2a)

Version

v1.0.3 (2020-02-24)

Developer

Mr. LI Hechen (GitHub)

Designer

Miss. Chen Lingxi (GitHub)
Dr. JIA Wenlong (Scholar, ORCID, GitHub)

Updates

v1.0.3

  • add gene annotations.
  • refine sidebar.
  • add highlights and tooltips on unit windows.
  • refine SV event information.
  • refine size of download figure.

v1.0.2

  • fix axis mapping.
  • add SV event information.
  • add chromosome for all region.
  • reset colorbar max value.

v1.0.1

  • fix color scheme.
  • fix axis coordinates overlaps.
  • optimize color scheme selection.
  • fix chromosome displays.

v1.0.0

  • initial functions implemented.
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