Please try the demo file in the sidebar (Demo File Sets).

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 an 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 the necessary information of the object that the mouse points to.
  • SV Point: Chromosome of 5' breakpoint, the position of 5' breakpoint, chromosome of 3' breakpoint, the 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 a dark background and the light theme with a light background.
• 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 events, show gene annotation, and so on.

• Files
  • Upload: upload heatmap TXT file, and manage uploaded files. Note that the duplicated file name will be alerted and given a random postfix.
  • Choose: choose files uploaded previously. Note that this function is ONLY available to the 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. Users can select the 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, the chromosome of 5' breakpoint, the position of 5' breakpoint, the chromosome of 3' breakpoint, the 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=1.0.5, written by Miss. CHEN Lingxi and Dr. JIA Wenlong on 2020-03-30.